101
|
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods 2021; 18:156-164. [PMID: 33542514 PMCID: PMC7864804 DOI: 10.1038/s41592-020-01051-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.
Collapse
Affiliation(s)
- Catherine L. Lawson
- grid.430387.b0000 0004 1936 8796Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Andriy Kryshtafovych
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California, Davis, CA USA
| | - Paul D. Adams
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Pavel V. Afonine
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Matthew L. Baker
- grid.267308.80000 0000 9206 2401Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX USA
| | - Benjamin A. Barad
- grid.214007.00000000122199231Department of Integrated Computational Structural Biology, The Scripps Research Institute, La Jolla, CA USA
| | - Paul Bond
- grid.5685.e0000 0004 1936 9668York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom Burnley
- grid.465239.fScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Renzhi Cao
- grid.261584.c0000 0001 0492 9915Department of Computer Science, Pacific Lutheran University, Tacoma, WA USA
| | - Jianlin Cheng
- grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA
| | - Grzegorz Chojnowski
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - Kevin Cowtan
- grid.5685.e0000 0004 1936 9668York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Ken A. Dill
- grid.36425.360000 0001 2216 9681Laufer Center, Stony Brook University, Stony Brook, NY USA
| | - Frank DiMaio
- grid.34477.330000000122986657Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA USA
| | - Daniel P. Farrell
- grid.34477.330000000122986657Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA USA
| | - James S. Fraser
- grid.266102.10000 0001 2297 6811Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA USA
| | - Mark A. Herzik
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA USA
| | - Soon Wen Hoh
- grid.5685.e0000 0004 1936 9668York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- grid.262962.b0000 0004 1936 9342Department of Computer Science, Saint Louis University, St. Louis, MO USA
| | - Li-Wei Hung
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM USA
| | - Maxim Igaev
- grid.418140.80000 0001 2104 4211Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Agnel P. Joseph
- grid.465239.fScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Daisuke Kihara
- grid.169077.e0000 0004 1937 2197Department of Biological Sciences, Purdue University, West Lafayette, IN USA ,grid.169077.e0000 0004 1937 2197Department of Computer Science, Purdue University, West Lafayette, IN USA
| | - Dilip Kumar
- grid.39382.330000 0001 2160 926XVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX USA
| | - Sumit Mittal
- grid.215654.10000 0001 2151 2636Biodesign Institute, Arizona State University, Tempe, AZ USA ,grid.411530.20000 0001 0694 3745School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Bohdan Monastyrskyy
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California, Davis, CA USA
| | - Mateusz Olek
- grid.5685.e0000 0004 1936 9668York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Colin M. Palmer
- grid.465239.fScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Ardan Patwardhan
- grid.225360.00000 0000 9709 7726The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Alberto Perez
- grid.15276.370000 0004 1936 8091Department of Chemistry, University of Florida, Gainesville, FL USA
| | - Jonas Pfab
- grid.462982.30000 0000 8883 2602Division of Computing & Software Systems, University of Washington, Bothell, WA USA
| | - Grigore D. Pintilie
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Jane S. Richardson
- grid.26009.3d0000 0004 1936 7961Department of Biochemistry, Duke University, Durham, NC USA
| | - Peter B. Rosenthal
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK
| | - Daipayan Sarkar
- grid.169077.e0000 0004 1937 2197Department of Biological Sciences, Purdue University, West Lafayette, IN USA ,grid.215654.10000 0001 2151 2636Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Luisa U. Schäfer
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Michael F. Schmid
- grid.168010.e0000000419368956Division of CryoEM and Biomaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| | - Gunnar F. Schröder
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- grid.215654.10000 0001 2151 2636Biodesign Institute, Arizona State University, Tempe, AZ USA ,grid.66859.34Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Dong Si
- grid.462982.30000 0000 8883 2602Division of Computing & Software Systems, University of Washington, Bothell, WA USA
| | - Abishek Singharoy
- grid.215654.10000 0001 2151 2636Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Genki Terashi
- grid.418140.80000 0001 2104 4211Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Andrea Vaiana
- grid.418140.80000 0001 2104 4211Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Liguo Wang
- grid.34477.330000000122986657Department of Biological Structure, University of Washington, Seattle, WA USA
| | - Zhe Wang
- grid.225360.00000 0000 9709 7726The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Stephanie A. Wankowicz
- grid.266102.10000 0001 2297 6811Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Biophysics Graduate Program, University of California, San Francisco, CA USA
| | | | - Martyn Winn
- grid.465239.fScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Tianqi Wu
- grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA
| | - Xiaodi Yu
- grid.497530.c0000 0004 0389 4927SMPS, Janssen Research and Development, Spring House, PA USA
| | - Kaiming Zhang
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Helen M. Berman
- grid.430387.b0000 0004 1936 8796Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA ,grid.42505.360000 0001 2156 6853Department of Biological Sciences and Bridge Institute, University of Southern California, Los Angeles, CA USA
| | - Wah Chiu
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Division of CryoEM and Biomaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| |
Collapse
|
102
|
Abstract
Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu ). The PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving data standards and data validation for improving data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve data quality and accommodate new data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metadata for all experimentally determined atomic structures, experimental data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.
Collapse
Affiliation(s)
- Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Genji Kurisu
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jeffrey C Hoch
- BioMagResBank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - John L Markley
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
103
|
Raimondi V, Grinzato A. A basic introduction to single particles cryo-electron microscopy. AIMS BIOPHYSICS 2021. [DOI: 10.3934/biophy.2022002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
<abstract>
<p>In the last years, cryogenic-electron microscopy (cryo-EM) underwent the most impressive improvement compared to other techniques used in structural biology, such as X-ray crystallography and NMR. Electron microscopy was invented nearly one century ago but, up to the beginning of the last decades, the 3D maps produced through this technique were poorly detailed, justifying the term “blobbology” to appeal to cryo-EM. Recently, thanks to a new generation of microscopes and detectors, more efficient algorithms, and easier access to computational power, single particles cryo-EM can routinely produce 3D structures at resolutions comparable to those obtained with X-ray crystallography. However, unlike X-ray crystallography, which needs crystallized proteins, cryo-EM exploits purified samples in solution, allowing the study of proteins and protein complexes that are hard or even impossible to crystallize. For these reasons, single-particle cryo-EM is often the first choice of structural biologists today. Nevertheless, before starting a cryo-EM experiment, many drawbacks and limitations must be considered. Moreover, in practice, the process between the purified sample and the final structure could be trickier than initially expected. Based on these observations, this review aims to offer an overview of the principal technical aspects and setups to be considered while planning and performing a cryo-EM experiment.</p>
</abstract>
Collapse
|
104
|
Kimanius D, Zickert G, Nakane T, Adler J, Lunz S, Schönlieb CB, Öktem O, Scheres SHW. Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination. IUCRJ 2021; 8:60-75. [PMID: 33520243 PMCID: PMC7793004 DOI: 10.1107/s2052252520014384] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/29/2020] [Indexed: 05/07/2023]
Abstract
Three-dimensional reconstruction of the electron-scattering potential of biological macromolecules from electron cryo-microscopy (cryo-EM) projection images is an ill-posed problem. The most popular cryo-EM software solutions to date rely on a regularization approach that is based on the prior assumption that the scattering potential varies smoothly over three-dimensional space. Although this approach has been hugely successful in recent years, the amount of prior knowledge that it exploits compares unfavorably with the knowledge about biological structures that has been accumulated over decades of research in structural biology. Here, a regularization framework for cryo-EM structure determination is presented that exploits prior knowledge about biological structures through a convolutional neural network that is trained on known macromolecular structures. This neural network is inserted into the iterative cryo-EM structure-determination process through an approach that is inspired by regularization by denoising. It is shown that the new regularization approach yields better reconstructions than the current state of the art for simulated data, and options to extend this work for application to experimental cryo-EM data are discussed.
Collapse
Affiliation(s)
- Dari Kimanius
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Gustav Zickert
- Department of Mathematics, Royal Institute of Technology (KTH), Sweden
| | - Takanori Nakane
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Sebastian Lunz
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Carola-Bibiane Schönlieb
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Ozan Öktem
- Department of Mathematics, Royal Institute of Technology (KTH), Sweden
| | | |
Collapse
|
105
|
Burley SK. Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. J Biol Chem 2021; 296:100559. [PMID: 33744282 PMCID: PMC8059052 DOI: 10.1016/j.jbc.2021.100559] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
The Protein Data Bank (PDB) is an international core data resource central to fundamental biology, biomedicine, bioenergy, and biotechnology/bioengineering. Now celebrating its 50th anniversary, the PDB houses >175,000 experimentally determined atomic structures of proteins, nucleic acids, and their complexes with one another and small molecules and drugs. The importance of three-dimensional (3D) biostructure information for research and education obtains from the intimate link between molecular form and function evident throughout biology. Among the most prolific consumers of PDB data are biomedical researchers, who rely on the open access resource as the authoritative source of well-validated, expertly curated biostructures. This review recounts how the PDB grew from just seven protein structures to contain more than 49,000 structures of human proteins that have proven critical for understanding their roles in human health and disease. It then describes how these structures are used in academe and industry to validate drug targets, assess target druggability, characterize how tool compounds and other small-molecules bind to drug targets, guide medicinal chemistry optimization of binding affinity and selectivity, and overcome challenges during preclinical drug development. Three case studies drawn from oncology exemplify how structural biologists and open access to PDB structures impacted recent regulatory approvals of antineoplastic drugs.
Collapse
Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, 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; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.
| |
Collapse
|
106
|
Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. SCIENCE ADVANCES 2021; 7:7/3/eabd4484. [PMID: 33523904 PMCID: PMC7810384 DOI: 10.1126/sciadv.abd4484] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/25/2020] [Indexed: 05/02/2023]
Abstract
The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.
Collapse
Affiliation(s)
- Yi-Chuan Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chia-En Chang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| |
Collapse
|
107
|
Sali A. From integrative structural biology to cell biology. J Biol Chem 2021; 296:100743. [PMID: 33957123 PMCID: PMC8203844 DOI: 10.1016/j.jbc.2021.100743] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ∼52-MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving integrative modeling include expanding model representations, increasing the variety of input data and prior information, quantifying a match between input information and a model in a Bayesian fashion, inventing more efficient structural sampling, as well as developing better model validation, analysis, and visualization. In addition, two community-level challenges in integrative modeling are being addressed under the auspices of the Worldwide Protein Data Bank (wwPDB). First, the impact of integrative structures is maximized by PDB-Development, a prototype wwPDB repository for archiving, validating, visualizing, and disseminating integrative structures. Second, the scope of structural biology is expanded by linking the wwPDB resource for integrative structures with archives of data that have not been generally used for structure determination but are increasingly important for computing integrative structures, such as data from various types of mass spectrometry, spectroscopy, optical microscopy, proteomics, and genetics. To address the largest of modeling problems, a type of integrative modeling called metamodeling is being developed; metamodeling combines different types of input models as opposed to different types of data to compute an output model. Collectively, these developments will facilitate the structural biology mindset in cell biology and underpin spatiotemporal mapping of the entire cell.
Collapse
Affiliation(s)
- Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, the Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
| |
Collapse
|
108
|
Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD. CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Crystallogr D Struct Biol 2021; 77:48-61. [PMID: 33404525 PMCID: PMC7787109 DOI: 10.1107/s2059798320015879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
Collapse
Affiliation(s)
- Dorothee Liebschner
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Vincent B. Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
109
|
Fowler NJ, Sljoka A, Williamson MP. A method for validating the accuracy of NMR protein structures. Nat Commun 2020; 11:6321. [PMID: 33339822 PMCID: PMC7749147 DOI: 10.1038/s41467-020-20177-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/13/2020] [Indexed: 01/13/2023] Open
Abstract
We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.
Collapse
Affiliation(s)
- Nicholas J Fowler
- Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Dept of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada.
| | - Mike P Williamson
- Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
| |
Collapse
|
110
|
Williamson LE, Gilliland T, Yadav PK, Binshtein E, Bombardi R, Kose N, Nargi RS, Sutton RE, Durie CL, Armstrong E, Carnahan RH, Walker LM, Kim AS, Fox JM, Diamond MS, Ohi MD, Klimstra WB, Crowe JE. Human Antibodies Protect against Aerosolized Eastern Equine Encephalitis Virus Infection. Cell 2020; 183:1884-1900.e23. [PMID: 33301709 DOI: 10.1016/j.cell.2020.11.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/23/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022]
Abstract
Eastern equine encephalitis virus (EEEV) is one of the most virulent viruses endemic to North America. No licensed vaccines or antiviral therapeutics are available to combat this infection, which has recently shown an increase in human cases. Here, we characterize human monoclonal antibodies (mAbs) isolated from a survivor of natural EEEV infection with potent (<20 pM) inhibitory activity of EEEV. Cryo-electron microscopy reconstructions of two highly neutralizing mAbs, EEEV-33 and EEEV-143, were solved in complex with chimeric Sindbis/EEEV virions to 7.2 Å and 8.3 Å, respectively. The mAbs recognize two distinct antigenic sites that are critical for inhibiting viral entry into cells. EEEV-33 and EEEV-143 protect against disease following stringent lethal aerosol challenge of mice with highly pathogenic EEEV. These studies provide insight into the molecular basis for the neutralizing human antibody response against EEEV and can facilitate development of vaccines and candidate antibody therapeutics.
Collapse
Affiliation(s)
- Lauren E Williamson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Theron Gilliland
- The Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 165261, USA
| | - Pramod K Yadav
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elad Binshtein
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel S Nargi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel E Sutton
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Clarissa L Durie
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erica Armstrong
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert H Carnahan
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren M Walker
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Arthur S Kim
- Department of Medicine, Washington University, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Julie M Fox
- Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - William B Klimstra
- The Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 165261, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 165261, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| |
Collapse
|
111
|
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe 2020; 28:867-879.e5. [PMID: 33271067 PMCID: PMC7670890 DOI: 10.1016/j.chom.2020.11.004] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
Collapse
Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jared M Sampson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
112
|
Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature 2020; 588:344-349. [PMID: 32814344 PMCID: PMC7726071 DOI: 10.1038/s41586-020-2673-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease1 and is also linked to its idiopathic form2. LRRK2 has been proposed to function in membrane trafficking3 and colocalizes with microtubules4. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure5. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
Collapse
Affiliation(s)
- C K Deniston
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - J Salogiannis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - S Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - D M Snead
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - I Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - M Matyszewski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - O Donosa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - R Watanabe
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - J Böhning
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - A K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - E Villa
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.
| | - A E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
113
|
Role of the Herpes Simplex Virus CVSC Proteins at the Capsid Portal Vertex. J Virol 2020; 94:JVI.01534-20. [PMID: 32967953 DOI: 10.1128/jvi.01534-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
The packaging of DNA into preformed capsids is a critical step during herpesvirus infection. For herpes simplex virus, this process requires the products of seven viral genes: the terminase proteins pUL15, pUL28, and pUL33; the capsid vertex-specific component (CVSC) proteins pUL17 and pUL25; and the portal proteins pUL6 and pUL32. The pUL6 portal dodecamer is anchored at one vertex of the capsid by interactions with the adjacent triplexes as well as helical density attributed to the pUL17 and pUL25 subunits of the CVSC. To define the roles and structures of the CVSC proteins in virus assembly and DNA packaging, we isolated a number of recombinant viruses expressing pUL25, pUL17, and pUL36 fused with green or red fluorescent proteins as well as viruses with specific deletions in the CVSC genes. Biochemical and structural studies of these mutants demonstrated that (i) four of the helices in the CVSC helix bundle can be attributed to two copies each of pUL36 and pUL25, (ii) pUL17 and pUL6 are required for capsid binding of the terminase complex in the nucleus, (iii) pUL17 is important for determining the site of the first cleavage reaction generating replicated genomes with termini derived from the long-arm component of the herpes simplex virus 1 (HSV-1) genome, (iv) pUL36 serves no direct role in cleavage/packaging, (v) cleavage and stable packaging of the viral genome involve an ordered interaction of the terminase complex and pUL25 with pUL17 at the portal vertex, and (vi) packaging of the viral genome results in a dramatic displacement of the portal.IMPORTANCE Herpes simplex virus 1 (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. A critical step during productive HSV-1 infection is the cleavage and packaging of replicated, concatemeric viral DNA into preformed capsids. A key knowledge gap is how the capsid engages the replicated viral genome and the subsequent packaging of a unit-length HSV genome. Here, biochemical and structural studies focused on the unique portal vertex of wild-type HSV and packaging mutants provide insights into the mechanism of HSV genome packaging. The significance of our research is in identifying the portal proteins pUL6 and pUL17 as key viral factors for engaging the terminase complex with the capsid and the subsequent cleavage, packaging, and stable incorporation of the viral genome in the HSV-1 capsid.
Collapse
|
114
|
Finogenova K, Bonnet J, Poepsel S, Schäfer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Müller J. Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3. eLife 2020; 9:e61964. [PMID: 33211010 PMCID: PMC7725500 DOI: 10.7554/elife.61964] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro. Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.
Collapse
Affiliation(s)
- Ksenia Finogenova
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Jacques Bonnet
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Simon Poepsel
- California Institute for Quantitative Biology (QB3), University of California, California Institute for Quantitative Biology (QB3), Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital CologneCologneGermany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of CologneCologneGermany
| | - Ingmar B Schäfer
- Max Planck Institute of Biochemistry, Department of Structural Cell BiologyMartinsriedGermany
| | - Katja Finkl
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Katharina Schmid
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Claudia Litz
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Mike Strauss
- Max Planck Institute of Biochemistry, cryoEM FacilityMartinsriedGermany
| | - Christian Benda
- Max Planck Institute of Biochemistry, Department of Structural Cell BiologyMartinsriedGermany
| | - Jürg Müller
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| |
Collapse
|
115
|
Stabrin M, Schoenfeld F, Wagner T, Pospich S, Gatsogiannis C, Raunser S. TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM. Nat Commun 2020; 11:5716. [PMID: 33177513 PMCID: PMC7658977 DOI: 10.1038/s41467-020-19513-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022] Open
Abstract
Single particle cryo-EM requires full automation to allow high-throughput structure determination. Although software packages exist where parts of the cryo-EM pipeline are automated, a complete solution that offers reliable on-the-fly processing, resulting in high-resolution structures, does not exist. Here we present TranSPHIRE: A software package for fully-automated processing of cryo-EM datasets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering, and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all metrics and microscope settings to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.
Collapse
Affiliation(s)
- Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Fabian Schoenfeld
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.
| |
Collapse
|
116
|
The structure of a red-shifted photosystem I reveals a red site in the core antenna. Nat Commun 2020; 11:5279. [PMID: 33077842 PMCID: PMC7573975 DOI: 10.1038/s41467-020-18884-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structure−function relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency. Cyanobacterial photosystem I has a highly conserved core antenna consisting of eleven subunits and more than 90 chlorophylls. Here via CryoEM and spectroscopy, the authors determine the location of a red-shifted low-energy chlorophyll that allows harvesting of longer wavelengths of light.
Collapse
|
117
|
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure 2020; 28:1259-1268. [PMID: 33065067 DOI: 10.1016/j.str.2020.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/02/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Cross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.
Collapse
|
118
|
Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G. Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Sci Rep 2020; 10:16301. [PMID: 33004869 PMCID: PMC7530986 DOI: 10.1038/s41598-020-73199-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/11/2020] [Indexed: 01/21/2023] Open
Abstract
Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
Collapse
Affiliation(s)
- Eileen L. Murphy
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Kavindra V. Singh
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Bryant Avila
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Torsten Kleffmann
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Steven T. Gregory
- grid.20431.340000 0004 0416 2242Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881 USA
| | - Barbara E. Murray
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Kurt L. Krause
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Reza Khayat
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Gerwald Jogl
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
| |
Collapse
|
119
|
Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2. Int J Mol Sci 2020; 21:ijms21197094. [PMID: 32993041 PMCID: PMC7584034 DOI: 10.3390/ijms21197094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Heterodimeric amino acid transporters (HATs) are protein complexes mediating the transport of amino acids and derivatives thereof across biological membranes. HATs are composed of two subunits, a heavy and a light chain subunit belonging to the solute carrier (SLC) families SLC3 and SLC7. The human HAT 4F2hc-LAT2 is composed of the type-II membrane N-glycoprotein 4F2hc (SCL3A2) and the L-type amino acid transporter LAT2 (SLC7A8), which are covalently linked to each other by a conserved disulfide bridge. Whereas LAT2 catalyzes substrate transport, 4F2hc is important for the successful trafficking of the transporter to the plasma membrane. The overexpression, malfunction, or absence of 4F2hc-LAT2 is associated with human diseases, and therefore, this heterodimeric complex represents a potential drug target. The recombinant human 4F2hc-LAT2 can be functionally overexpressed in the methylotrophic yeast Pichia pastoris, and the protein can be purified. Here, we present the cryo-EM density map of the human 4F2hc-LAT2 amino acid transporter at sub-nanometer resolution. A homology model of 4F2hc-LAT2 in the inward-open conformation was generated and fitted into the cryo-EM density and analyzed. In addition, disease-causing point mutations in human LAT2 were mapped on the homology model of 4F2hc-LAT2, and the possible functional implications on the molecular level are discussed.
Collapse
|
120
|
Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
Collapse
Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| |
Collapse
|
121
|
Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JH. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:60482. [PMID: 32924932 DOI: 10.1101/2020.06.26.174334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 05/24/2023] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
Collapse
Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, United States
| | - Jamie Hd Cate
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
122
|
Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JHD. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:e60482. [PMID: 32924932 PMCID: PMC7550191 DOI: 10.7554/elife.60482] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
Collapse
Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
| | - Omer Ad
- Department of Chemistry, Yale UniversityNew HavenUnited States
| | - Alanna Schepartz
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
- Environmental Science, Policy and Management, University of California BerkeleyBerkeleyUnited States
| | - Jamie HD Cate
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| |
Collapse
|
123
|
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure 2020; 28:1249-1258.e2. [PMID: 32857966 DOI: 10.1016/j.str.2020.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/23/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022]
Abstract
Ramachandran plots report the distribution of the (ϕ, ψ) torsion angles of the protein backbone and are one of the best quality metrics of experimental structure models. Typically, validation software reports the number of residues belonging to "outlier," "allowed," and "favored" regions. While "zero unexplained outliers" can be considered the current "gold standard," this can be misleading if deviations from expected distributions are not considered. We revisited the Ramachandran Z score (Rama-Z), a quality metric introduced more than two decades ago but underutilized. We describe a reimplementation of the Rama-Z score in the Computational Crystallography Toolbox along with an algorithm to estimate its uncertainty for individual models; final implementations are available in Phenix and PDB-REDO. We discuss the interpretation of the Rama-Z score and advocate including it in the validation reports provided by the Protein Data Bank. We also advocate reporting it alongside the outlier/allowed/favored counts in structural publications.
Collapse
|
124
|
Hankaniemi MM, Baikoghli MA, Stone VM, Xing L, Väätäinen O, Soppela S, Sioofy-Khojine A, Saarinen NVV, Ou T, Anson B, Hyöty H, Marjomäki V, Flodström-Tullberg M, Cheng RH, Hytönen VP, Laitinen OH. Structural Insight into CVB3-VLP Non-Adjuvanted Vaccine. Microorganisms 2020; 8:microorganisms8091287. [PMID: 32846899 PMCID: PMC7565060 DOI: 10.3390/microorganisms8091287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Coxsackievirus B (CVB) enteroviruses are common pathogens that can cause acute and chronic myocarditis, dilated cardiomyopathy, aseptic meningitis, and they are hypothesized to be a causal factor in type 1 diabetes. The licensed enterovirus vaccines and those currently in clinical development are traditional inactivated or live attenuated vaccines. Even though these vaccines work well in the prevention of enterovirus diseases, new vaccine technologies, like virus-like particles (VLPs), can offer important advantages in the manufacturing and epitope engineering. We have previously produced VLPs for CVB3 and CVB1 in insect cells. Here, we describe the production of CVB3-VLPs with enhanced production yield and purity using an improved purification method consisting of tangential flow filtration and ion exchange chromatography, which is compatible with industrial scale production. We also resolved the CVB3-VLP structure by Cryo-Electron Microscopy imaging and single particle reconstruction. The VLP diameter is 30.9 nm on average, and it is similar to Coxsackievirus A VLPs and the expanded enterovirus cell-entry intermediate (the 135s particle), which is ~2 nm larger than the mature virion. High neutralizing and total IgG antibody levels, the latter being a predominantly Th2 type (IgG1) phenotype, were detected in C57BL/6J mice immunized with non-adjuvanted CVB3-VLP vaccine. The structural and immunogenic data presented here indicate the potential of this improved methodology to produce highly immunogenic enterovirus VLP-vaccines in the future.
Collapse
Affiliation(s)
- Minna M. Hankaniemi
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
- Correspondence: (M.M.H.); (V.P.H.); Tel.: +358-504176882 (M.M.H.); +358-401901517 (V.P.H.)
| | - Mo A. Baikoghli
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; (M.A.B.); (L.X.); (T.O.); (B.A.); (R.H.C.)
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, P.O. Box 20, University of Helsinki, 00014 Helsinki, Finland
| | - Virginia M. Stone
- The Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 52 Stockholm, Sweden; (V.M.S.); (M.F.-T.)
| | - Li Xing
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; (M.A.B.); (L.X.); (T.O.); (B.A.); (R.H.C.)
| | - Outi Väätäinen
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
| | - Saana Soppela
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
| | - Amirbabak Sioofy-Khojine
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
| | - Niila V. V. Saarinen
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
| | - Tingwei Ou
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; (M.A.B.); (L.X.); (T.O.); (B.A.); (R.H.C.)
| | - Brandon Anson
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; (M.A.B.); (L.X.); (T.O.); (B.A.); (R.H.C.)
| | - Heikki Hyöty
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
- Fimlab Laboratories, FI-33520 Tampere, Finland
| | - Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland;
| | - Malin Flodström-Tullberg
- The Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 52 Stockholm, Sweden; (V.M.S.); (M.F.-T.)
| | - R. Holland Cheng
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; (M.A.B.); (L.X.); (T.O.); (B.A.); (R.H.C.)
| | - Vesa P. Hytönen
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
- Fimlab Laboratories, FI-33520 Tampere, Finland
- Correspondence: (M.M.H.); (V.P.H.); Tel.: +358-504176882 (M.M.H.); +358-401901517 (V.P.H.)
| | - Olli H. Laitinen
- Faculty of Medicine and Life Sciences, Tampere University, FI-33014 Tampere, Finland; (O.V.); (S.S.); (A.S.-K.); (N.V.V.S.); (H.H.); (O.H.L.)
| |
Collapse
|
125
|
A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation. Nat Commun 2020; 11:4141. [PMID: 32811830 PMCID: PMC7435202 DOI: 10.1038/s41467-020-17911-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/21/2020] [Indexed: 11/24/2022] Open
Abstract
Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.
Collapse
|
126
|
Wang Y, Han Y, She J, Nguyen NX, Mootha VK, Bai XC, Jiang Y. Structural insights into the Ca 2+-dependent gating of the human mitochondrial calcium uniporter. eLife 2020; 9:e60513. [PMID: 32762847 PMCID: PMC7442490 DOI: 10.7554/elife.60513] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial Ca2+ uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, MICU1 and MICU2, among which MCU and EMRE form a subcomplex and function as the conductive channel while MICU1 and MICU2 are EF-hand proteins that regulate the channel activity in a Ca2+-dependent manner. Here, we present the EM structures of the human mitochondrial calcium uniporter holocomplex (uniplex) in the presence and absence of Ca2+, revealing distinct Ca2+ dependent assembly of the uniplex. Our structural observations suggest that Ca2+ changes the dimerization interaction between MICU1 and MICU2, which in turn determines how the MICU1-MICU2 subcomplex interacts with the MCU-EMRE channel and, consequently, changes the distribution of the uniplex assemblies between the blocked and unblocked states.
Collapse
Affiliation(s)
- Yan Wang
- Department of Physiology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yan Han
- Department of Physiology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nam X Nguyen
- Department of Physiology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Broad InstituteCambridgeUnited States
| | - Xiao-chen Bai
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| |
Collapse
|
127
|
Abstract
During global pandemics, the spread of information needs to be faster than the spread of the virus in order to ensure the health and safety of human populations worldwide. In our current crisis, the demand for SARS-CoV-2 drugs and vaccines highlights the importance of biological targets and their three-dimensional shape. In particular, structural biology as a field was poised to quickly respond to crises due to previous experience and expertise and because of its early adoption of open access practices.
Collapse
Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
128
|
Ramlaul K, Palmer CM, Nakane T, Aylett CHS. Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER. J Struct Biol 2020; 211:107545. [PMID: 32534144 PMCID: PMC7369633 DOI: 10.1016/j.jsb.2020.107545] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 01/31/2023]
Abstract
Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such "over-fitting" can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins.
Collapse
Affiliation(s)
- Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom
| | - Colin M Palmer
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Takanori Nakane
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom.
| |
Collapse
|
129
|
Zhou T, Tsybovsky Y, Olia AS, Gorman J, Rapp MA, Cerutti G, Chuang GY, Katsamba PS, Nazzari A, Sampson JM, Schon A, Wang PD, Bimela J, Shi W, Teng IT, Zhang B, Boyington JC, Sastry M, Stephens T, Stuckey J, Wang S, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Cryo-EM Structures Delineate a pH-Dependent Switch that Mediates Endosomal Positioning of SARS-CoV-2 Spike Receptor-Binding Domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637958 DOI: 10.1101/2020.07.04.187989] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the ACE2 receptor and to facilitate virus entry. Antibodies can engage RBD but some, such as CR3022, fail to inhibit entry despite nanomolar spike affinity. Here we show the SARS-CoV-2 spike to have low unfolding enthalpy at serological pH and up to 10-times more unfolding enthalpy at endosomal pH, where we observe significantly reduced CR3022 affinity. Cryo-EM structures -at serological and endosomal pH- delineated spike recognition of up to three ACE2 molecules, revealing RBD to freely adopt the 'up' conformation. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a locked all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning and spike shedding of antibodies like CR3022. An endosomal mechanism involving spike-conformational change can thus facilitate immune evasion from RBD-'up'-recognizing antibody.
Collapse
|
130
|
Ortiz S, Stanisic L, Rodriguez BA, Rampp M, Hummer G, Cossio P. Validation tests for cryo-EM maps using an independent particle set. J Struct Biol X 2020; 4:100032. [PMID: 32743544 PMCID: PMC7385033 DOI: 10.1016/j.yjsbx.2020.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data. Here, we develop a novel methodology that uses a small independent particle set (not used during the 3D refinement) to validate the maps. The main idea is to monitor how the map probability evolves over the control set during the 3D refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and the refinement iteration. We also compute the similarity between the densities of probability distributions of the two reconstructions. As higher frequencies are included, the distributions become more dissimilar. We optimized the BioEM package to perform these calculations, and tested it over systems ranging from quality data to pure noise. Our results show that with our methodology, it possible to discriminate datasets that are constructed from noise particles. We conclude that validation against a control particle set provides a powerful tool to assess the quality of cryo-EM maps.
Collapse
Affiliation(s)
- Sebastian Ortiz
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Luka Stanisic
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Boris A Rodriguez
- Grupo de Fósica Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Markus Rampp
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University, 60438 Frankfurt am Main, Germany
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| |
Collapse
|
131
|
Yu X, Yi P, Hamilton RA, Shen H, Chen M, Foulds CE, Mancini MA, Ludtke SJ, Wang Z, O'Malley BW. Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes. Mol Cell 2020; 79:812-823.e4. [PMID: 32668201 DOI: 10.1016/j.molcel.2020.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 01/15/2023]
Abstract
Steroid receptors activate gene transcription by recruiting coactivators to initiate transcription of their target genes. For most nuclear receptors, the ligand-dependent activation function domain-2 (AF-2) is a primary contributor to the nuclear receptor (NR) transcriptional activity. In contrast to other steroid receptors, such as ERα, the activation function of androgen receptor (AR) is largely dependent on its ligand-independent AF-1 located in its N-terminal domain (NTD). It remains unclear why AR utilizes a different AF domain from other receptors despite that NRs share similar domain organizations. Here, we present cryoelectron microscopy (cryo-EM) structures of DNA-bound full-length AR and its complex structure with key coactivators, SRC-3 and p300. AR dimerization follows a unique head-to-head and tail-to-tail manner. Unlike ERα, AR directly contacts a single SRC-3 and p300. The AR NTD is the primary site for coactivator recruitment. The structures provide a basis for understanding assembly of the AR:coactivator complex and its domain contributions for coactivator assembly and transcriptional regulation.
Collapse
Affiliation(s)
- Xinzhe Yu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hong Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven J Ludtke
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhao Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
132
|
Berman HM, Vallat B, Lawson CL. The data universe of structural biology. IUCRJ 2020; 7:630-638. [PMID: 32695409 PMCID: PMC7340255 DOI: 10.1107/s205225252000562x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/21/2020] [Indexed: 05/05/2023]
Abstract
The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.
Collapse
Affiliation(s)
- Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biological Sciences and Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Brinda Vallat
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
133
|
Joseph AP, Lagerstedt I, Jakobi A, Burnley T, Patwardhan A, Topf M, Winn M. Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps. J Chem Inf Model 2020; 60:2552-2560. [PMID: 32043355 PMCID: PMC7254831 DOI: 10.1021/acs.jcim.9b01103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is a powerful technique for determining structures of multiple conformational or compositional states of macromolecular assemblies involved in cellular processes. Recent technological developments have led to a leap in the resolution of many cryo-EM data sets, making atomic model building more common for data interpretation. We present a method for calculating differences between two cryo-EM maps or a map and a fitted atomic model. The proposed approach works by scaling the maps using amplitude matching in resolution shells. To account for variability in local resolution of cryo-EM data, we include a procedure for local amplitude scaling that enables appropriate scaling of local map contrast. The approach is implemented as a user-friendly tool in the CCP-EM software package. To obtain clean and interpretable differences, we propose a protocol involving steps to process the input maps and output differences. We demonstrate the utility of the method for identifying conformational and compositional differences including ligands. We also highlight the use of difference maps for evaluating atomic model fit in cryo-EM maps.
Collapse
Affiliation(s)
- Agnel Praveen Joseph
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ingvar Lagerstedt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Arjen Jakobi
- Kavli Institute of Nanoscience Delft (KIND), Department of Bionanoscienes, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Tom Burnley
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| |
Collapse
|
134
|
Capsid Structure of a Marine Algal Virus of the Order Picornavirales. J Virol 2020; 94:JVI.01855-19. [PMID: 32024776 DOI: 10.1128/jvi.01855-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first alga virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, revealed that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. The above-mentioned and other critical structural features provide new insights on three long-standing theories about Picornavirales: (i) the canyon hypothesis, (ii) the primordial VP2 domain swap, and (iii) the hypothesis that alga Picornavirales viruses could share characteristics with the Picornavirales ancestor.IMPORTANCE Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes and thus still share some characteristics with the Picornavirales ancestor. This article describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.
Collapse
|
135
|
Fang Q, Tang WC, Tao P, Mahalingam M, Fokine A, Rossmann MG, Rao VB. Structural morphing in a symmetry-mismatched viral vertex. Nat Commun 2020; 11:1713. [PMID: 32249784 PMCID: PMC7136217 DOI: 10.1038/s41467-020-15575-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 11/26/2022] Open
Abstract
Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion. In icosahedral viruses, a symmetry-mismatched portal vertex is assembled by inserting a 12-fold-symmetric portal complex into a 5-fold-symmetric capsid environment. Here, the authors report a near-atomic-resolution in situ cryo-electron microscopy structure of this symmetrically mismatched viral vertex from bacteriophage T4.
Collapse
Affiliation(s)
- Qianglin Fang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Wei-Chun Tang
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Pan Tao
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Marthandan Mahalingam
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA.
| |
Collapse
|
136
|
Chen L, He J. Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. Molecules 2020; 25:E1540. [PMID: 32231015 PMCID: PMC7181022 DOI: 10.3390/molecules25071540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/16/2020] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0-4 Å and 4-6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing sets of X-ray structures derived from different resolution ranges-higher than 1.5 Å, 1.5-2.0 Å, 2.0-2.5 Å, 2.5-3.0 Å, and 3.0-3.5 Å. The overall quality of cryo-EM structures is likely improved, as shown in a comparison of cryo-EM structures released before the end of 2016, those between 2017 and 2018, and those between 2018 and 2019. Our investigation shows that leucine (LEU) has a significantly higher rate of HBOS outliers than that of the reference data set (X-ray-1.5) and of other residue types in the cryo-EM data sets. HBOS was able to detect outliers for those residues that are currently marked as green in PDB validation reports. Conclusions: The HBOS profile of a dataset is a potential method to characterize the overall structural quality of the set. Residue LEU deserves special attention since it has a significantly higher HBOS outlier rate in sets of cryo-EM structures and those X-ray structures derived from X-ray data of lower than 2.5 Å resolutions. Most HBOS outlier residues from the EM-0-4-2019 set are located on loops for most types of residues.
Collapse
Affiliation(s)
- Lin Chen
- Department of Computer Science, Valdosta State University, 1500 N Patterson St, Valdosta, GA 31698, USA
| | - Jing He
- Department of Computer Science, Old Dominion University, 5115 Hampton Blvd, Norfolk, VA 23529, USA;
| |
Collapse
|
137
|
Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 2020; 177:1384-1403. [PMID: 31150619 DOI: 10.1016/j.cell.2019.05.016] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
Collapse
Affiliation(s)
- Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
138
|
Carlino E. In-Line Holography in Transmission Electron Microscopy for the Atomic Resolution Imaging of Single Particle of Radiation-Sensitive Matter. MATERIALS 2020; 13:ma13061413. [PMID: 32245011 PMCID: PMC7142924 DOI: 10.3390/ma13061413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Abstract
In this paper, for the first time it is shown how in-line holography in Transmission Electron Microscopy (TEM) enables the study of radiation-sensitive nanoparticles of organic and inorganic materials providing high-contrast holograms of single nanoparticles, while illuminating specimens with a density of current as low as 1–2 e−Å−2s−1. This provides a powerful method for true single-particle atomic resolution imaging and opens up new perspectives for the study of soft matter in biology and materials science. The approach is not limited to a particular class of TEM specimens, such as homogenous samples or samples specially designed for a particular TEM experiment, but has better application in the study of those specimens with differences in shape, chemical composition, crystallography, and orientation, which cannot be currently addressed at atomic resolution.
Collapse
Affiliation(s)
- Elvio Carlino
- Istituto per la Microelettronica ed i Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM), Sezione di Lecce, Campus Universitario, via per Monteroni, 73100 Lecce, Italy
| |
Collapse
|
139
|
Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation. Proc Natl Acad Sci U S A 2020; 117:4931-4941. [PMID: 32075920 PMCID: PMC7060699 DOI: 10.1073/pnas.1919837117] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.
Collapse
|
140
|
Han Y, Reyes AA, Malik S, He Y. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature 2020; 579:452-455. [PMID: 32188938 PMCID: PMC7319049 DOI: 10.1038/s41586-020-2087-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair1,2. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers3-8, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation9.
Collapse
Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alexis A Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA
| | - Sara Malik
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
| |
Collapse
|
141
|
Poudyal I, Schmidt M, Schwander P. Single-particle imaging by x-ray free-electron lasers-How many snapshots are needed? STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024102. [PMID: 32232074 PMCID: PMC7088463 DOI: 10.1063/1.5144516] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense x-ray pulses that are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns, the three-dimensional electron density of a molecule can be reconstructed ab initio. The quality of the reconstruction depends largely on the number of patterns collected at the experiment. This paper provides an estimate of the number of diffraction patterns required to reconstruct the electron density at a targeted spatial resolution. This estimate is verified by simulations for realistic x-ray fluences, repetition rates, and experimental conditions available at modern XFELs. Employing the bacterial phytochrome as a model system, we demonstrate that sub-nanometer resolution is within reach.
Collapse
Affiliation(s)
| | | | - P. Schwander
- Author to whom correspondence should be addressed:
| |
Collapse
|
142
|
Abstract
Cross-validation is used to determine the validity of a model on unseen data by assessing if the model is overfitted to noise. It is widely used in many fields, from artificial intelligence to structural biology in X-ray crystallography and nuclear magnetic resonance. Although there are concerns of map overfitting in cryo-electron microscopy (cryo-EM), cross-validation is rarely used. The problem is that establishing a performance metric of the maps over unseen data (given by 2D-projection images) is difficult due to the low signal-to-noise ratios in the individual particles. Here, I present recent advances for cryo-EM map reconstruction. I highlight that the gold-standard procedure can fail to detect map overfitting in certain cases, showing the necessity of assessing the map quality on unbiased data. Finally, I describe the challenges and advantages of developing a robust cross-validation methodology for cryo-EM.
Collapse
Affiliation(s)
- Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| |
Collapse
|
143
|
Kyrilis FL, Meister A, Kastritis PL. Integrative biology of native cell extracts: a new era for structural characterization of life processes. Biol Chem 2020; 400:831-846. [PMID: 31091193 DOI: 10.1515/hsz-2018-0445] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Advances in electron microscopy have provided unprecedented access to the structural characterization of large, flexible and heterogeneous complexes. Until recently, cryo-electron microscopy (cryo-EM) has been applied to understand molecular organization in either highly purified, isolated biomolecules or in situ. An emerging field is developing, bridging the gap between the two approaches, and focuses on studying molecular organization in native cell extracts. This field has demonstrated its potential by resolving the structure of fungal fatty acid synthase (FAS) at 4.7 Å [Fourier shell correlation (FSC) = 0.143]; FAS was not only less than 50% enriched, but also retained higher-order binders, previously unknown. Although controversial in the sense that the lysis step might introduce artifacts, cell extracts preserve aspects of cellular function. In addition, cell extracts are accessible, besides cryo-EM, to modern proteomic methods, chemical cross-linking, network biology and biophysical modeling. We expect that automation in imaging cell extracts, along with the integration of molecular/cell biology approaches, will provide remarkable achievements in the study of closer-to-life biomolecular states of pronounced biotechnological and medical importance. Such steps will, eventually, bring us a step closer to the biophysical description of cellular processes in an integrative, holistic approach.
Collapse
Affiliation(s)
- Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany.,Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, D-06120 Halle/Saale, Germany
| |
Collapse
|
144
|
Wang Z, Hu W, Zheng H. Pathogenic siderophore ABC importer YbtPQ adopts a surprising fold of exporter. SCIENCE ADVANCES 2020; 6:eaay7997. [PMID: 32076651 PMCID: PMC7002159 DOI: 10.1126/sciadv.aay7997] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/22/2019] [Indexed: 05/05/2023]
Abstract
To fight for essential metal ions, human pathogens secrete virulence-associated siderophores and retake the metal-chelated siderophores through a subfamily of adenosine triphosphate (ATP)-binding cassette (ABC) importer, whose molecular mechanisms are completely unknown. We have determined multiple structures of the yersiniabactin importer YbtPQ from uropathogenic Escherichia coli (UPEC) at inward-open conformation in both apo and substrate-bound states by cryo-electron microscopy. YbtPQ does not adopt any known fold of ABC importers but surprisingly adopts the fold of type IV ABC exporters. To our knowledge, it is the first time an exporter fold of ABC importer has been reported. We have also observed two unique features in YbtPQ: unwinding of a transmembrane helix in YbtP upon substrate release and tightly associated nucleotide-binding domains without bound nucleotides. Together, our study suggests that siderophore ABC importers have a distinct transport mechanism and should be classified as a separate subfamily of ABC importers.
Collapse
|
145
|
Moscovich A, Halevi A, Andén J, Singer A. Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes. INVERSE PROBLEMS 2020; 36:024003. [PMID: 32394996 PMCID: PMC7213598 DOI: 10.1088/1361-6420/ab4f55] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts that move and deform. Traditional reconstruction methods fail in these cases, resulting in smeared reconstructions of the moving parts. This poses a major obstacle for structural biologists, who need high-resolution reconstructions of entire macromolecules, moving parts included. To address this challenge, we present a new method for the reconstruction of macromolecules exhibiting continuous heterogeneity. The proposed method uses projection images from multiple viewing directions to construct a graph Laplacian through which the manifold of three-dimensional conformations is analyzed. The 3D molecular structures are then expanded in a basis of Laplacian eigenvectors, using a novel generalized tomographic reconstruction algorithm to compute the expansion coefficients. These coefficients, which we name spectral volumes, provide a high-resolution visualization of the molecular dynamics. We provide a theoretical analysis and evaluate the method empirically on several simulated data sets.
Collapse
Affiliation(s)
- Amit Moscovich
- Program in Applied & Computational Mathematics, Princeton University, Princeton, NJ
| | - Amit Halevi
- Program in Applied & Computational Mathematics, Princeton University, Princeton, NJ
| | - Joakim Andén
- Center for Computational Mathematics, Flatiron Institute, New York, NY
| | - Amit Singer
- Program in Applied & Computational Mathematics, Princeton University, Princeton, NJ
- Department of Mathematics, Princeton University, Princeton, NJ
| |
Collapse
|
146
|
Vilas JL, Vargas J, Martinez M, Ramirez-Aportela E, Melero R, Jimenez-Moreno A, Garduño E, Conesa P, Marabini R, Maluenda D, Carazo JM, Sorzano COS. Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening. J Struct Biol 2020; 209:107447. [PMID: 31911170 DOI: 10.1016/j.jsb.2020.107447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/29/2019] [Accepted: 01/01/2020] [Indexed: 11/24/2022]
Abstract
The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.
Collapse
Affiliation(s)
- J L Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Vargas
- Dept. Anatomy and Cell Biology, McGill Univ., Montreal, Canada
| | - M Martinez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramirez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jimenez-Moreno
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Garduño
- Department of Computer Science, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - P Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Escuela Politecnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - D Maluenda
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Monteprincipe, 28668 Boadilla del Monte, Madrid, Spain.
| |
Collapse
|
147
|
Lawson CL, Berman HM, Chiu W. Evolving data standards for cryo-EM structures. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014701. [PMID: 32002441 PMCID: PMC6980868 DOI: 10.1063/1.5138589] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.
Collapse
Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | | | | |
Collapse
|
148
|
Ayyer K, Morgan AJ, Aquila A, DeMirci H, Hogue BG, Kirian RA, Xavier PL, Yoon CH, Chapman HN, Barty A. Low-signal limit of X-ray single particle diffractive imaging. OPTICS EXPRESS 2019; 27:37816-37833. [PMID: 31878556 DOI: 10.1364/oe.27.037816] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single snapshot and instrument background may be significant relative to particle scattering. While analyses of simulated data have shown that the determination of an average image should be feasible using Bayesian methods such as the EMC algorithm, this has yet to be demonstrated using experimental data containing realistic non-isotropic instrument background, sample variability and other experimental factors. In this work, we show that the orientation and phase retrieval steps work at photon counts diluted to the signal levels one expects from smaller molecules or with weaker pulses, using data from experimental measurements of 60-nm PR772 viruses. Even when the signal is reduced to a fraction as little as 1/256, the virus electron density determined using ab initio phasing is of almost the same quality as the high-signal data. However, we are still limited by the total number of patterns collected, which may soon be mitigated by the advent of high repetition-rate sources like the European XFEL and LCLS-II.
Collapse
|
149
|
Jiang D, Shi H, Tonggu L, Gamal El-Din TM, Lenaeus MJ, Zhao Y, Yoshioka C, Zheng N, Catterall WA. Structure of the Cardiac Sodium Channel. Cell 2019; 180:122-134.e10. [PMID: 31866066 DOI: 10.1016/j.cell.2019.11.041] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/18/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channel Nav1.5 generates cardiac action potentials and initiates the heartbeat. Here, we report structures of NaV1.5 at 3.2-3.5 Å resolution. NaV1.5 is distinguished from other sodium channels by a unique glycosyl moiety and loss of disulfide-bonding capability at the NaVβ subunit-interaction sites. The antiarrhythmic drug flecainide specifically targets the central cavity of the pore. The voltage sensors are partially activated, and the fast-inactivation gate is partially closed. Activation of the voltage sensor of Domain III allows binding of the isoleucine-phenylalanine-methionine (IFM) motif to the inactivation-gate receptor. Asp and Ala, in the selectivity motif DEKA, line the walls of the ion-selectivity filter, whereas Glu and Lys are in positions to accept and release Na+ ions via a charge-delocalization network. Arrhythmia mutation sites undergo large translocations during gating, providing a potential mechanism for pathogenic effects. Our results provide detailed insights into Nav1.5 structure, pharmacology, activation, inactivation, ion selectivity, and arrhythmias.
Collapse
Affiliation(s)
- Daohua Jiang
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Hui Shi
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Lige Tonggu
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yan Zhao
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Craig Yoshioka
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
150
|
Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y. Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor. eLife 2019; 8:50928. [PMID: 31846423 PMCID: PMC6917491 DOI: 10.7554/elife.50928] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
σS is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σS-mediated transcription requires a σS-specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an Escherichia coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σS-RNA polymerase (σS-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σS (σS2) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σS2 to promote the assembly of the σS-RNAP holoenzyme and also to facilitate formation of an RNA polymerase–promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.
Collapse
Affiliation(s)
- Juncao Xu
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaijie Cui
- University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Liqiang Shen
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingting Li
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linlin You
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chengli Fang
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,Department of Microbiology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, China.,State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China.,Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|