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Goodsell DS, Dutta S, Hudson BP, Voigt M, Burley SK, Zardecki C. Folding paper models of biostructures for outreach and education. Patterns (N Y) 2024; 5:100931. [PMID: 38370120 PMCID: PMC10873190 DOI: 10.1016/j.patter.2024.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Molecular origami offers an offline way to explore the 3D structures of biology. Visit PDB101.rcsb.org to download free paper models of DNA, green fluorescent protein, viruses, and more.
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Affiliation(s)
- David S. Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Research Collaboratory for Structural Biology Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Turner J, Abbott S, Fonseca N, Pye R, Carrijo L, Duraisamy AK, Salih O, Wang Z, Kleywegt GJ, Morris KL, Patwardhan A, Burley SK, Crichlow G, Feng Z, Flatt JW, Ghosh S, Hudson BP, Lawson CL, Liang Y, Peisach E, Persikova I, Sekharan M, Shao C, Young J, Velankar S, Armstrong D, Bage M, Bueno WM, Evans G, Gaborova R, Ganguly S, Gupta D, Harrus D, Tanweer A, Bansal M, Rangannan V, Kurisu G, Cho H, Ikegawa Y, Kengaku Y, Kim JY, Niwa S, Sato J, Takuwa A, Yu J, Hoch JC, Baskaran K, Xu W, Zhang W, Ma X. EMDB-the Electron Microscopy Data Bank. Nucleic Acids Res 2024; 52:D456-D465. [PMID: 37994703 PMCID: PMC10767987 DOI: 10.1093/nar/gkad1019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.
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Flatt JW, Hudson BP, Persikova I, Liang Y, Shao C, Peisach E, Young JY, Burley SK. Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank. Microsc Microanal 2023; 29:948. [PMID: 37613801 DOI: 10.1093/micmic/ozad067.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Justin W Flatt
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Brian P Hudson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Irina Persikova
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Yuhe Liang
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Chenghua Shao
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Ezra Peisach
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, United States
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, California, United States
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Lubin JH, Martinusen SG, Zardecki C, Olivas C, Bacorn M, Balogun M, Slaton EW, Wu AW, Sakeer S, Hudson BP, Denard CA, Burley SK, Khare SD. A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic. bioRxiv 2023:2023.01.30.526101. [PMID: 36778399 PMCID: PMC9915488 DOI: 10.1101/2023.01.30.526101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although the rapid development of therapeutic responses to combat SARS-CoV-2 represents a great human achievement, it also demonstrates untapped potential for advanced pandemic preparedness. Cross-species efficacy against multiple human coronaviruses by the main protease (MPro) inhibitor nirmatrelvir raises the question of its breadth of inhibition and our preparedness against future coronaviral threats. Herein, we describe sequence and structural analyses of 346 unique MPro enzymes from all coronaviruses represented in the NCBI Virus database. Cognate substrates of these representative proteases were inferred from their polyprotein sequences. We clustered MPro sequences based on sequence identity and AlphaFold2-predicted structures, showing approximate correspondence with known viral subspecies. Predicted structures of five representative MPros bound to their inferred cognate substrates showed high conservation in protease:substrate interaction modes, with some notable differences. Yeast-based proteolysis assays of the five representatives were able to confirm activity of three on inferred cognate substrates, and demonstrated that of the three, only one was effectively inhibited by nirmatrelvir. Our findings suggest that comprehensive preparedness against future potential coronaviral threats will require continued inhibitor development. Our methods may be applied to candidate coronaviral MPro inhibitors to evaluate in advance the breadth of their inhibition and identify target coronaviruses potentially meriting advanced development of alternative countermeasures.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | | | - Christine Zardecki
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Cassandra Olivas
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- California State University Stanislaus, Turlock, California, USA
| | - Mickayla Bacorn
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- University Of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - MaryAgnes Balogun
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Morgan State University, Baltimore, Maryland, USA
| | - Ethan W. Slaton
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Amy Wu Wu
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- University of Puerto Rico – Mayagüez, Mayagüez, Puerto Rico
| | - Sarah Sakeer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Brian P. Hudson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Carl A. Denard
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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5
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Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Res 2023; 51:D488-D508. [PMID: 36420884 PMCID: PMC9825554 DOI: 10.1093/nar/gkac1077] [Citation(s) in RCA: 119] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Sebastian Bittrich
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Henry Chao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Li Chen
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Paul A Craig
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Gregg V Crichlow
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kenneth Dalenberg
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Maryam Fayazi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Justin W Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sai Ganesan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David S Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rachel Kramer Green
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Vladimir Guranovic
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jeremy Henry
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Igor Khokhriakov
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dennis W Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ben Webb
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Shamara Whetstone
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Arthur Zalevsky
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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6
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Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 2022; 14:1281-1301. [PMID: 36474933 PMCID: PMC9715422 DOI: 10.1007/s12551-022-01013-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/06/2022] [Indexed: 12/04/2022] Open
Abstract
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| | - Wei Dai
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901 USA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | | | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158 USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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7
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Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein Sci 2022; 31:e4482. [PMID: 36281733 PMCID: PMC9667899 DOI: 10.1002/pro.4482] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Cancer Institute of New Jersey, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA,Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA,Department of Chemistry and Chemical Biology, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Sebastian Bittrich
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Henry Chao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Li Chen
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Paul A. Craig
- School of Chemistry and Materials ScienceRochester Institute of TechnologyRochesterNew YorkUSA
| | - Gregg V. Crichlow
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Kenneth Dalenberg
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Cancer Institute of New Jersey, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Maryam Fayazi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Sai J. Ganesan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic SciencesQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Pharmaceutical ChemistryQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - David S. Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Cancer Institute of New Jersey, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA,Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Rachel Kramer Green
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vladimir Guranovic
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jeremy Henry
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Igor Khokhriakov
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Dennis W. Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic SciencesQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Pharmaceutical ChemistryQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of CaliforniaLa JollaCaliforniaUSA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Benjamin Webb
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic SciencesQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Pharmaceutical ChemistryQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shamara Whetstone
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Arthur Zalevsky
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic SciencesQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Pharmaceutical ChemistryQuantitative Biosciences Institute, University of CaliforniaSan FranciscoCaliforniaUSA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
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8
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Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 2022; 12:1425. [PMID: 36291635 PMCID: PMC9599165 DOI: 10.3390/biom12101425] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dennis W. Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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9
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Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie‐Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz‐Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Proteins 2022; 90:1054-1080. [PMID: 34580920 PMCID: PMC8661935 DOI: 10.1002/prot.26250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023]
Abstract
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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Affiliation(s)
- Joseph H. Lubin
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Elliott M. Dolan
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zhuofan Shen
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shuchismita Dutta
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - John D. Westbrook
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Brian P. Hudson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - David S. Goodsell
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- The Scripps Research InstituteLa JollaCaliforniaUSA
| | - Jonathan K. Williams
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vidur Sarma
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Lingjun Xie
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Thejasvi Venkatachalam
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Steven Arnold
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | - Aaliyah Khan
- University of Maryland Baltimore CountyBaltimoreMarylandUSA
| | | | | | | | | | | | | | - Helen Zheng
- Watchung Hills Regional High SchoolWarrenNew JerseyUSA
| | | | | | - Mark Dresel
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | | | | | - Evan Lenkeit
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | - Andrew Sam
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Katherine See
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Paul A. Craig
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Jennifer Jiang
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Jay Tischfield
- Department of GeneticsRutgers, The State University of New Jersey, and Human Genetics Institute of New JerseyPiscatawayNew JerseyUSA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Eddy Arnold
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jean Baum
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jesse Sandberg
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Grace Brannigan
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
- Department of PhysicsRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
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10
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Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Kramer Green R, Guranovic V, Henry J, Hudson BP, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Whetstone S, Young JY, Zardecki C. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Sci 2022; 31:187-208. [PMID: 34676613 PMCID: PMC8740825 DOI: 10.1002/pro.4213] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Sebastian Bittrich
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Li Chen
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Gregg V. Crichlow
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Maryam Fayazi
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Sai J. Ganesan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences InstituteUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - David S. Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Rachel Kramer Green
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vladimir Guranovic
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jeremy Henry
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Dennis W. Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences InstituteUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Shamara Whetstone
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
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11
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Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Christie CH, Dalenberg K, Di Costanzo L, Duarte JM, Dutta S, Feng Z, Ganesan S, Goodsell DS, Ghosh S, Green RK, Guranović V, Guzenko D, Hudson BP, Lawson C, Liang Y, Lowe R, Namkoong H, Peisach E, Persikova I, Randle C, Rose A, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Tao YP, Voigt M, Westbrook J, Young JY, Zardecki C, Zhuravleva M. RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Res 2021; 49:D437-D451. [PMID: 33211854 PMCID: PMC7779003 DOI: 10.1093/nar/gkaa1038] [Citation(s) in RCA: 731] [Impact Index Per Article: 243.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Sebastian Bittrich
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Li Chen
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gregg V Crichlow
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Cole H Christie
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Kenneth Dalenberg
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Luigi Di Costanzo
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sai Ganesan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David S Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Center for Computational Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rachel Kramer Green
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Vladimir Guranović
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dmytro Guzenko
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Harry Namkoong
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chris Randle
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Alexander Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yi-Ping Tao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jasmine Y Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marina Zhuravleva
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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12
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Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MOA, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic. bioRxiv 2020. [PMID: 33299989 DOI: 10.1101/2020.12.01.406637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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13
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Burley SK, Bromberg Y, Craig P, Duffy S, Dutta S, Hall BL, Hudson BP, Jiang J, D Khare S, Koeppe JR, Lubin JH, Mills SA, Pikaart MJ, Roberts R, Sarma V, Singh J, Tischfield JA, Xie L, Zardecki C. Virtual Boot Camp: COVID-19 evolution and structural biology. Biochem Mol Biol Educ 2020; 48:511-513. [PMID: 32797732 PMCID: PMC7590104 DOI: 10.1002/bmb.21428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 05/25/2023]
Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of California, San DiegoLa JollaCaliforniaUSA
- Rutgers Cancer Institute of New Jersey, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew JerseyUSA
| | - Paul Craig
- School of Chemistry & Materials ScienceRochester Institute of TechnologyRochesterNew YorkUSA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Bonnie L. Hall
- Department of ChemistryGrand View UniversityDes MoinesIowaUSA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Jennifer Jiang
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Sagar D Khare
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry & Chemical BiologyRutgers UniversityPiscatawayNew JerseyUSA
| | - Julia R. Koeppe
- ChemistryState University of New York at OswegoOswegoNew YorkUSA
| | - Joseph H. Lubin
- Department of Chemistry & Chemical BiologyRutgers UniversityPiscatawayNew JerseyUSA
| | | | | | - Rebecca Roberts
- Biology DepartmentUrsinus CollegeCollegevillePennsylvaniaUSA
| | - Vidur Sarma
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Jitendra Singh
- CUNY New York City College of TechnologyNew YorkNew YorkUSA
| | - Jay A. Tischfield
- Department of GeneticsRutgers UniversityPiscatawayNew JerseyUSA
- Human Genetics Institute of New JerseyPiscatawayNew JerseyUSA
| | - Lingjun Xie
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
- Institute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNew JerseyUSA
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14
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Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Di Costanzo L, Christie C, Dalenberg K, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Kalro T, Liang Y, Lowe R, Namkoong H, Peisach E, Periskova I, Prlic A, Randle C, Rose A, Rose P, Sala R, Sekharan M, Shao C, Tan L, Tao YP, Valasatava Y, Voigt M, Westbrook J, Woo J, Yang H, Young J, Zhuravleva M, Zardecki C. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res 2020; 47:D464-D474. [PMID: 30357411 PMCID: PMC6324064 DOI: 10.1093/nar/gky1004] [Citation(s) in RCA: 717] [Impact Index Per Article: 179.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chunxiao Bi
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Chen
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Luigi Di Costanzo
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Cole Christie
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ken Dalenberg
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David S Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rachel K Green
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Vladimir Guranovic
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dmytro Guzenko
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Tara Kalro
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Harry Namkoong
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Periskova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andreas Prlic
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chris Randle
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Raul Sala
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Lihua Tan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yi-Ping Tao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Valasatava
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jesse Woo
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Huanwang Yang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marina Zhuravleva
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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15
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Westbrook JD, Soskind R, Hudson BP, Burley SK. Impact of the Protein Data Bank on antineoplastic approvals. Drug Discov Today 2020; 25:837-850. [PMID: 32068073 DOI: 10.1016/j.drudis.2020.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Open access to 3D structure information from the Protein Data Bank (PDB) facilitated discovery and development of >90% of the 79 new antineoplastic agents (54 small molecules, 25 biologics) with known molecular targets approved by the FDA 2010-2018. Analyses of PDB holdings, the scientific literature and related documents for each drug-target combination revealed that the impact of public-domain 3D structure data was broad and substantial, ranging from understanding target biology (∼95% of all targets) to identifying a given target as probably druggable (∼95% of all targets) to structure-guided lead optimization (>70% of all small-molecule drugs). In addition to aggregate impact assessments, illustrative case studies are presented for three protein kinase inhibitors, an allosteric enzyme inhibitor and seven advanced-stage melanoma therapeutics.
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Affiliation(s)
- John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rose Soskind
- Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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16
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Goodsell DS, Zardecki C, Di Costanzo L, Duarte JM, Hudson BP, Persikova I, Segura J, Shao C, Voigt M, Westbrook JD, Young JY, Burley SK. RCSB Protein Data Bank: Enabling biomedical research and drug discovery. Protein Sci 2019; 29:52-65. [PMID: 31531901 DOI: 10.1002/pro.3730] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022]
Abstract
Analyses of publicly available structural data reveal interesting insights into the impact of the three-dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G-protein-coupled receptors, voltage-gated ion channels, ligand-gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic-level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open-access, digital-data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ∼40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ∼90% of the 210 new drugs approved by the US Food and Drug Administration 2010-2016. We review user-driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure-guided drug discovery for challenging targets (e.g., integral membrane proteins).
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Affiliation(s)
- David S Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,The Scripps Research Institute, La Jolla, California
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Luigi Di Costanzo
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Jasmine Y Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
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17
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Miller B, Hudson BP, Shao C, Wang L, Zardecki C, Burley SK. Improving Ligand Geometry in Protein Data Bank Structures Computationally. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.784.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Beck Miller
- Smith CollegeNorthamptonMA
- RCSB PDBThe State University of New JerseyPiscatawayNJ
| | - Brian P Hudson
- RCSB PDBThe State University of New JerseyPiscatawayNJ
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNJ
| | - Chenghua Shao
- RCSB PDBThe State University of New JerseyPiscatawayNJ
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNJ
| | - Lu Wang
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNJ
| | - Christine Zardecki
- RCSB PDBThe State University of New JerseyPiscatawayNJ
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNJ
| | - Stephen K. Burley
- RCSB PDBThe State University of New JerseyPiscatawayNJ
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNJ
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18
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Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, Christie C, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Liang Y, Lowe R, Peisach E, Periskova I, Randle C, Rose A, Sekharan M, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook J, Young J, Zardecki C, Zhuravleva M, Kurisu G, Nakamura H, Kengaku Y, Cho H, Sato J, Kim JY, Ikegawa Y, Nakagawa A, Yamashita R, Kudou T, Bekker GJ, Suzuki H, Iwata T, Yokochi M, Kobayashi N, Fujiwara T, Velankar S, Kleywegt GJ, Anyango S, Armstrong DR, Berrisford JM, Conroy MJ, Dana JM, Deshpande M, Gane P, Gáborová R, Gupta D, Gutmanas A, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Patwardhan A, Paysan-Lafosse T, Pravda L, Salih O, Sehnal D, Varadi M, Vařeková R, Markley JL, Hoch JC, Romero PR, Baskaran K, Maziuk D, Ulrich EL, Wedell JR, Yao H, Livny M, Ioannidis YE. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 2019; 47:D520-D528. [PMID: 30357364 PMCID: PMC6324056 DOI: 10.1093/nar/gky949] [Citation(s) in RCA: 505] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 01/10/2023] Open
Abstract
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
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19
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Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database (Oxford) 2018; 2018:4844086. [PMID: 29688351 PMCID: PMC5804564 DOI: 10.1093/database/bay002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/02/2018] [Indexed: 11/24/2022]
Abstract
The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
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Affiliation(s)
- Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Irina Persikova
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Raul Sala
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - G Jawahar Swaminathan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Reiko Igarashi
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - David R Armstrong
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kumaran Baskaran
- BMRB, BioMagResBank, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Li Chen
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Minyu Chen
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Alice R Clark
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luigi Di Costanzo
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Dimitris Dimitropoulos
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Guanghua Gao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Sutapa Ghosh
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Vladimir Guranovic
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Yumiko Kengaku
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Yuhe Liang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Buvaneswari Narayanan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Kayoko Nishiyama
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eduardo Sanz-García
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Junko Sato
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Oliver S Smart
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Lihua Tan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Glen van Ginkel
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Marina A Zhuravleva
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Genji Kurisu
- PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.,RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Little Albany St, New Brunswick, NJ 08901, USA
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20
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Lawson CL, Gabanyi MJ, Westbrook J, Young J, Dutta S, Peisach E, Hudson BP, Rose P, Duarte J, Sarjeant A, Burley SK, Berman HM. New online curriculum: the PDB pipeline and data archiving. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Validation of Structures in the Protein Data Bank. Structure 2017; 25:1916-1927. [PMID: 29174494 PMCID: PMC5718880 DOI: 10.1016/j.str.2017.10.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/08/2017] [Accepted: 10/27/2017] [Indexed: 11/01/2022]
Abstract
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.
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Affiliation(s)
- Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eduardo Sanz García
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kumaran Baskaran
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Oliver S Smart
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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22
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Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure 2017; 25:536-545. [PMID: 28190782 DOI: 10.1016/j.str.2017.01.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/08/2016] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
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Affiliation(s)
- Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Raul Sala
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - David R Armstrong
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Li Chen
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Minyu Chen
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Luigi Di Costanzo
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dimitris Dimitropoulos
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Guanghua Gao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sutapa Ghosh
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Vladimir Guranovic
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Reiko Igarashi
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuhe Liang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - M Saqib Mir
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Irina Persikova
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Luana Rinaldi
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Eduardo Sanz-Garcia
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - G Jawahar Swaminathan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Lihua Tan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Glen van Ginkel
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marina A Zhuravleva
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
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23
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Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. EMDataBank unified data resource for 3DEM. Nucleic Acids Res 2015; 44:D396-403. [PMID: 26578576 PMCID: PMC4702818 DOI: 10.1093/nar/gkv1126] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/10/2023] Open
Abstract
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Corey Hryc
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Eduardo Sanz Garcia
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Grigore Pintilie
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Raul Sala
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - John D Westbrook
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
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Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA. Small molecule annotation for the Protein Data Bank. Database (Oxford) 2014; 2014:bau116. [PMID: 25425036 PMCID: PMC4243272 DOI: 10.1093/database/bau116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.
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Affiliation(s)
- Sanchayita Sen
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Jasmine Young
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Minyu Chen
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Matthew J Conroy
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Shuchismita Dutta
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Luigi Di Costanzo
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Guanghua Gao
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Sutapa Ghosh
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Brian P Hudson
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Reiko Igarashi
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Yumiko Kengaku
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Yuhe Liang
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Ezra Peisach
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Irina Persikova
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Buvaneswari Coimbatore Narayanan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Junko Sato
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Monica Sekharan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Chenghua Shao
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Lihua Tan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Marina A Zhuravleva
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
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Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C. Trendspotting in the Protein Data Bank. FEBS Lett 2013; 587:1036-45. [PMID: 23337870 PMCID: PMC4068610 DOI: 10.1016/j.febslet.2012.12.029] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/20/2012] [Accepted: 12/22/2012] [Indexed: 01/20/2023]
Abstract
The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA.
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Ho MX, Hudson BP, Das K, Arnold E, Ebright RH. Structures of RNA polymerase-antibiotic complexes. Curr Opin Struct Biol 2009; 19:715-23. [PMID: 19926275 DOI: 10.1016/j.sbi.2009.10.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 10/19/2009] [Accepted: 10/20/2009] [Indexed: 01/22/2023]
Abstract
Inhibition of bacterial RNA polymerase (RNAP) is an established strategy for antituberculosis therapy and broad-spectrum antibacterial therapy. Crystal structures of RNAP-inhibitor complexes are available for four classes of antibiotics: rifamycins, sorangicin, streptolydigin, and myxopyronin. The structures define three different targets, and three different mechanisms, for inhibition of bacterial RNAP: (1) rifamycins and sorangicin bind near the RNAP active center and block extension of RNA products; (2) streptolydigin interacts with a target that overlaps the RNAP active center and inhibits conformational cycling of the RNAP active center; and (3) myxopyronin interacts with a target remote from the RNAP active center and functions by interfering with opening of the RNAP active-center cleft to permit entry and unwinding of DNA and/or by interfering with interactions between RNAP and the DNA template strand. The structures enable construction of homology models of pathogen RNAP-antibiotic complexes, enable in silico screening for new antibacterial agents, and enable rational design of improved antibacterial agents.
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Affiliation(s)
- Mary X Ho
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, USA
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Hudson BP, Martinez-Yamout MA, Dyson HJ, Wright PE. Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat Struct Mol Biol 2004; 11:257-64. [PMID: 14981510 DOI: 10.1038/nsmb738] [Citation(s) in RCA: 282] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Accepted: 01/14/2004] [Indexed: 01/19/2023]
Abstract
The tandem zinc finger (TZF) domain of the protein TIS11d binds to the class II AU-rich element (ARE) in the 3' untranslated region (3' UTR) of target mRNAs and promotes their deadenylation and degradation. The NMR structure of the TIS11d TZF domain bound to the RNA sequence 5'-UUAUUUAUU-3' comprises a pair of novel CCCH fingers of type CX(8)CX(5)CX(3)H separated by an 18-residue linker. The two TIS11d zinc fingers bind in a symmetrical fashion to adjacent 5'-UAUU-3' subsites on the single-stranded RNA via a combination of electrostatic and hydrogen-bonding interactions, with intercalative stacking between conserved aromatic side chains and the RNA bases. Sequence specificity in RNA recognition is achieved by a network of intermolecular hydrogen bonds, mostly between TIS11d main-chain functional groups and the Watson-Crick edges of the bases. The TIS11d structure provides insights into the RNA-binding functions of this large family of CCCH zinc finger proteins.
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Affiliation(s)
- Brian P Hudson
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Hudson BP, Dupureur CM, Barton JK. 1H NMR Structural Evidence for the Sequence-Specific Design of an Intercalator: .DELTA.-.alpha.-[Rh[(R,R)-Me2trien]phi]3+ Bound to d(GAGTGCACTC)2. J Am Chem Soc 2002. [DOI: 10.1021/ja00141a041] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Krotz AH, Hudson BP, Barton JK. Assembly of DNA recognition elements on an octahedral rhodium intercalator: predictive recognition of 5'-TGCA-3' by .DELTA.-[Rh(R,R)-Me2trien]phi]3+. J Am Chem Soc 2002. [DOI: 10.1021/ja00079a044] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Meadows KA, Liu F, Hudson BP, McMillin DR. A monophenyl phenanthroline complex of copper(I) that binds to DNA but not by intercalation. Inorg Chem 2002. [DOI: 10.1021/ic00073a035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Meadows KA, Liu F, Sou J, Hudson BP, McMillin DR. Spectroscopic and photophysical studies of the binding interactions between copper phenanthroline complexes and RNA. Inorg Chem 2002. [DOI: 10.1021/ic00065a020] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The solution structure of the bromodomain from the human transcriptional coactivator GCN5 has been determined using NMR methods. The structure has a left-handed four-helix bundle topology, with two short additional helices in a long connecting loop. A hydrophobic groove and deep hydrophobic cavity are formed by loops at one end of the molecule. NMR binding experiments show that the cavity forms a specific binding pocket for the acetamide moiety. Peptides containing an N(epsilon)-acetylated lysine residue bind in this pocket with modest affinity (K(D) approximately 0.9 mM); no comparable binding occurs with unacetylated peptides. The GCN5 bromodomain binds the small ligands N(omega)-acetylhistamine and N-methylacetamide, confirming specificity for the alkyl acetamide moiety and showing that the primary element of recognition is simply the sterically unhindered terminal acetamide moiety of an acetylated lysine residue. Additional experiments show that binding is enhanced if the acetyl-lysine residue occurs within the context of a basic peptide and is inhibited by the presence of nearby acidic residues and by the carboxyl group of the free acetyl-lysine amino acid. The binding of the GCN5 bromodomain to acetylated peptides appears to have little additional sequence dependence, although weak interactions with other regions of the peptide are implicated by the binding data. Discrimination between ligands of positive and negative charge is attributed to the presence of several acidic residues located on the loops that form the sides of the binding pocket. Unlike the residues forming the acetamide binding cavity, these acidic side-chains are not conserved in other bromodomain sequences, suggesting that bromodomains might display differences in substrate selectivity and specificity as well as differences in function in vivo.
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Affiliation(s)
- B P Hudson
- The Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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Kielkopf CL, Erkkila KE, Hudson BP, Barton JK, Rees DC. Structure of a photoactive rhodium complex intercalated into DNA. Nat Struct Biol 2000; 7:117-21. [PMID: 10655613 DOI: 10.1038/72385] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 A resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix provides a rationale for the sequence specificity of rhodium intercalators. It also explains how intercalation in the center of an oligonucleotide modifies DNA conformation. The rhodium complex intercalates via the major groove where specific contacts are formed with the edges of the bases at the target site. The phi ligand is deeply inserted into the DNA base pair stack. The primary conformational change of the DNA is a doubling of the rise per residue, with no change in sugar pucker from B-form DNA. Based upon the five crystallographically independent views of an intercalated DNA helix observed in this structure, the intercalator may be considered as an additional base pair with specific functional groups positioned in the major groove.
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Affiliation(s)
- C L Kielkopf
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Affiliation(s)
- Brian P. Hudson
- Contribution from the Division of Chemistry & Chemical Engineering and the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Jacqueline K. Barton
- Contribution from the Division of Chemistry & Chemical Engineering and the Beckman Institute, California Institute of Technology, Pasadena, California 91125
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Hudson BP, Dupureur CM, Barton JK. 1H-NMR studies of an octahedral rhodium intercalator with designed DNA site-specificity. J Inorg Biochem 1995. [DOI: 10.1016/0162-0134(95)97270-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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