1
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods 2024; 21:1340-1348. [PMID: 38918604 DOI: 10.1038/s41592-024-02321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L Lawson
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | | | - Grigore D Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K Burley
- RCSB Protein Data Bank and 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
- RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Vincent B Chen
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- , Berlin, Germany
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Protein Science, Septerna, South San Francisco, CA, USA
| | | | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Alexis L Rohou
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Benjamin D Sellers
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- Computational Chemistry, Vilya, South San Francisco, CA, USA
| | - Chenghua Shao
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Venkat Abbaraju
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - K D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- The Chinese University of Hong Kong, Hong Kong, China
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Robert A Nicholls
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Luisa U Schäfer
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature's Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
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2
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Bochtler M. X-rays, electrons, and neutrons as probes of atomic matter. Structure 2024; 32:630-643.e6. [PMID: 38412856 DOI: 10.1016/j.str.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/21/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
X-rays, electrons, and neutrons probe different properties of matter. X-rays feel electron density (ED). Electrons sense the electrostatic potential (ESP) of electrons and nuclei. Neutrons are sensitive to nuclear coherent scattering length (NCSL). While NCSL maps are widely understood to be different, ED and ESP maps are tacitly assumed to be similar. Here, I show that the belief in ED and ESP map equivalence is mistaken, but contains a grain of truth. Using density functional theory (DFT), the Bethe-Mott (BM) relation, and the Thomas-Fermi (TF) and Cromer-Mann (CM) atomic models, I show that ED and ESP maps are indeed more similar to each other than to NCSL maps. Nevertheless, peak and integrated map values depend differently on the atomic order number and on the contributions from electrons in the inner and outer CM shells. ED and ESP maps also differ in the sign and relative magnitude of excess charge effects.
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Affiliation(s)
- Matthias Bochtler
- IIMCB, Trojdena 4, 02-109 Warsaw, Poland; Polish Academy of Sciences, IBB, Pawinskiego 5a, 02-106 Warsaw, Poland.
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3
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Nakagawa T, Wang XT, Miguez-Cabello FJ, Bowie D. The open gate of the AMPA receptor forms a Ca 2+ binding site critical in regulating ion transport. Nat Struct Mol Biol 2024; 31:688-700. [PMID: 38409505 DOI: 10.1038/s41594-024-01228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating mechanism has been studied extensively, understanding how cations traverse the pore has remained elusive. Here we investigated putative ion and water densities in the open pore of Ca2+-permeable AMPARs (rat GRIA2 flip-Q isoform) at 2.3-2.6 Å resolution. We show that the ion permeation pathway attains an extracellular Ca2+ binding site (site-G) when the channel gate moves into the open configuration. Site-G is highly selective for Ca2+ over Na+, favoring the movement of Ca2+ into the selectivity filter of the pore. Seizure-related N619K mutation, adjacent to site-G, promotes channel opening but attenuates Ca2+ binding and thus diminishes Ca2+ permeability. Our work identifies the importance of site-G, which coordinates with the Q/R site of the selectivity filter to ensure the preferential transport of Ca2+ through the channel pore.
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Affiliation(s)
- Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, TN, USA.
| | - Xin-Tong Wang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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4
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
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5
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ARXIV 2024:arXiv:2311.17640v3. [PMID: 38076521 PMCID: PMC10705588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D Adams
- Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA
| | | | - Catherine L Lawson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | - Maya Topf
- Birkbeck, University of London, London, UK
| | | | | | | | | | | | | | | | - Sai J Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John D Westbrook
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Martyn D Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
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6
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Dickerson JL, Leahy E, Peet MJ, Naydenova K, Russo CJ. Accurate magnification determination for cryoEM using gold. Ultramicroscopy 2024; 256:113883. [PMID: 38008055 PMCID: PMC10782223 DOI: 10.1016/j.ultramic.2023.113883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.
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Affiliation(s)
- Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Erin Leahy
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mathew J Peet
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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7
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. RESEARCH SQUARE 2024:rs.3.rs-3864137. [PMID: 38343795 PMCID: PMC10854310 DOI: 10.21203/rs.3.rs-3864137/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | - Grigore D. Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K. Burley
- 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
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc, South San Francisco, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc, South San Francisco, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Chenghua Shao
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc, South San Francisco, USA
| | - Venkat Abbaraju
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L. Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F. Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P. Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R. Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luisa U. Schäfer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J. Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F. Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C. Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature’s Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D. Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F. Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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8
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Böhning J, Dobbelstein AW, Sulkowski N, Eilers K, von Kügelgen A, Tarafder AK, Peak-Chew SY, Skehel M, Alva V, Filloux A, Bharat TAM. Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa. PLoS Pathog 2023; 19:e1011177. [PMID: 37058467 PMCID: PMC10104325 DOI: 10.1371/journal.ppat.1011177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/03/2023] [Indexed: 04/15/2023] Open
Abstract
Chaperone-Usher Pathway (CUP) pili are major adhesins in Gram-negative bacteria, mediating bacterial adherence to biotic and abiotic surfaces. While classical CUP pili have been extensively characterized, little is known about so-called archaic CUP pili, which are phylogenetically widespread and promote biofilm formation by several human pathogens. In this study, we present the electron cryomicroscopy structure of the archaic CupE pilus from the opportunistic human pathogen Pseudomonas aeruginosa. We show that CupE1 subunits within the pilus are arranged in a zigzag architecture, containing an N-terminal donor β-strand extending from each subunit into the next, where it is anchored by hydrophobic interactions, with comparatively weaker interactions at the rest of the inter-subunit interface. Imaging CupE pili on the surface of P. aeruginosa cells using electron cryotomography shows that CupE pili adopt variable curvatures in response to their environment, which might facilitate their role in promoting cellular attachment. Finally, bioinformatic analysis shows the widespread abundance of cupE genes in isolates of P. aeruginosa and the co-occurrence of cupE with other cup clusters, suggesting interdependence of cup pili in regulating bacterial adherence within biofilms. Taken together, our study provides insights into the architecture of archaic CUP pili, providing a structural basis for understanding their role in promoting cellular adhesion and biofilm formation in P. aeruginosa.
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Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Adrian W. Dobbelstein
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Nina Sulkowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Kira Eilers
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Abul K. Tarafder
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sew-Yeu Peak-Chew
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Tanmay A. M. Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
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9
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Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and
cryo‐electron
microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joseph George Beton
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck and University College London London UK
| | - Manaz Kaleel
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
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10
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Joseph AP, Malhotra S, Burnley T, Winn MD. Overview and applications of map and model validation tools in the CCP-EM software suite. Faraday Discuss 2022; 240:196-209. [PMID: 35916020 PMCID: PMC9642004 DOI: 10.1039/d2fd00103a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings.
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Affiliation(s)
- Agnel Praveen Joseph
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Sony Malhotra
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Tom Burnley
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Martyn D. Winn
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
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11
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Puskar R, Du Truong C, Swain K, Chowdhury S, Chan KY, Li S, Cheng KW, Wang TY, Poh YP, Mazor Y, Liu H, Chou TF, Nannenga BL, Chiu PL. Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria. Nat Commun 2022; 13:5824. [PMID: 36192412 PMCID: PMC9529944 DOI: 10.1038/s41467-022-33505-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.
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Affiliation(s)
- Ryan Puskar
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Chloe Du Truong
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Rampart Bioscience, Monrovia, CA, 91016, USA
| | - Kyle Swain
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Saborni Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Ka-Yi Chan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ting Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yu-Ping Poh
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Yuval Mazor
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Haijun Liu
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Brent L Nannenga
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
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12
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Chaaban S, Carter AP. Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Nature 2022; 610:212-216. [PMID: 36071160 PMCID: PMC7613678 DOI: 10.1038/s41586-022-05186-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor1-3. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour4-6. Different coiled-coil adaptors are linked to different cargos7,8, and some share motifs known to contact sites on dynein and dynactin4,9-13. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.
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Affiliation(s)
- Sami Chaaban
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P Carter
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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13
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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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14
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Buchanan CJ, Gaunt B, Harrison PJ, Yang Y, Liu J, Khan A, Giltrap AM, Le Bas A, Ward PN, Gupta K, Dumoux M, Tan TK, Schimaski L, Daga S, Picchiotti N, Baldassarri M, Benetti E, Fallerini C, Fava F, Giliberti A, Koukos PI, Davy MJ, Lakshminarayanan A, Xue X, Papadakis G, Deimel LP, Casablancas-Antràs V, Claridge TDW, Bonvin AMJJ, Sattentau QJ, Furini S, Gori M, Huo J, Owens RJ, Schaffitzel C, Berger I, Renieri A, Naismith JH, Baldwin AJ, Davis BG. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 2022; 377:eabm3125. [PMID: 35737812 DOI: 10.1126/science.abm3125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.
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Affiliation(s)
- Charles J Buchanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Ben Gaunt
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Peter J Harrison
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Yun Yang
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Jiwei Liu
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Aziz Khan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew M Giltrap
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Audrey Le Bas
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Philip N Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lisa Schimaski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthew J Davy
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Abirami Lakshminarayanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Xiaochao Xue
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Sir William Dunn School of Pathology, Oxford, UK
| | | | | | - Virgínia Casablancas-Antràs
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | | | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | | | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Gori
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Maasai, I3S CNRS, Université Côte d'Azur, Nice, France
| | - Jiandong Huo
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J Owens
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Christiane Schaffitzel
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Imre Berger
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Andrew J Baldwin
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Benjamin G Davis
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
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15
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Gilles MA, Singer A. A molecular prior distribution for Bayesian inference based on Wilson statistics. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106830. [PMID: 35537297 PMCID: PMC9233040 DOI: 10.1016/j.cmpb.2022.106830] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Wilson statistics describe well the power spectrum of proteins at high frequencies. Therefore, it has found several applications in structural biology, e.g., it is the basis for sharpening steps used in cryogenic electron microscopy (cryo-EM). A recent paper gave the first rigorous proof of Wilson statistics based on a formalism of Wilson's original argument. This new analysis also leads to statistical estimates of the scattering potential of proteins that reveal a correlation between neighboring Fourier coefficients. Here we exploit these estimates to craft a novel prior that can be used for Bayesian inference of molecular structures. METHODS We describe the properties of the prior and the computation of its hyperparameters. We then evaluate the prior on two synthetic linear inverse problems, and compare against a popular prior in cryo-EM reconstruction at a range of SNRs. RESULTS We show that the new prior effectively suppresses noise and fills-in low SNR regions in the spectral domain. Furthermore, it improves the resolution of estimates on the problems considered for a wide range of SNR and produces Fourier Shell Correlation curves that are insensitive to masking effects. CONCLUSIONS We analyze the assumptions in the model, discuss relations to other regularization strategies, and postulate on potential implications for structure determination in cryo-EM.
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Affiliation(s)
- Marc Aurèle Gilles
- Program in Applied and Computational Mathematics, Princeton University, Fine Hall, Washington Road, Princeton, NJ 08544-1000, United States.
| | - Amit Singer
- Department of Mathematics and PACM, Princeton University, Fine Hall, Washington Road, Princeton, NJ 08544-1000, United States
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Wang Z, Patwardhan A, Kleywegt GJ. Validation analysis of EMDB entries. Acta Crystallogr D Struct Biol 2022; 78:542-552. [PMID: 35503203 PMCID: PMC9063848 DOI: 10.1107/s205979832200328x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for the validation of cryo-EM structures, focusing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested metrics as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as nonspecialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. The details of the new resource are described, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to obtain a better understanding of the quality and of the best ways to assess the quality of cryo-EM structures in EMDB and PDB.
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Affiliation(s)
- Zhe Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Gerard J. Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
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Stagnoli S, Peccati F, Connell SR, Martinez-Castillo A, Charro D, Millet O, Bruzzone C, Palazon A, Ardá A, Jiménez-Barbero J, Ereño-Orbea J, Abrescia NGA, Jiménez-Osés G. Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods. Front Microbiol 2022; 13:870938. [PMID: 35495643 PMCID: PMC9053831 DOI: 10.3389/fmicb.2022.870938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two years after its emergence, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several vaccines. The extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin converting enzyme 2 (ACE2) through its receptor binding domain (RBD), is the major target of neutralizing antibodies. Like to many other viral fusion proteins, the SARS-CoV-2 spike protein utilizes a glycan shield to thwart the host immune response. To grasp the influence of chemical signatures on carbohydrate mobility and reconcile the cryo-EM density of specific glycans we combined our cryo-EM map of the S ectodomain to 4.1 Å resolution, reconstructed from a limited number of particles, and all-atom molecular dynamics simulations. Chemical modifications modeled on representative glycans (defucosylation, sialylation and addition of terminal LacNAc units) show no significant influence on either protein shielding or glycan flexibility. By estimating at selected sites the local correlation between the full density map and atomic model-based maps derived from molecular dynamics simulations, we provide insight into the geometries of the α-Man-(1→3)-[α-Man-(1→6)-]-β-Man-(1→4)-β-GlcNAc(1→4)-β-GlcNAc core common to all N-glycosylation sites.
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Affiliation(s)
- Soledad Stagnoli
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Francesca Peccati
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Sean R. Connell
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Martinez-Castillo
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Diego Charro
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Asis Palazon
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ana Ardá
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Jesús Jiménez-Barbero
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - June Ereño-Orbea
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Nicola G. A. Abrescia,
| | - Gonzalo Jiménez-Osés
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Gonzalo Jiménez-Osés,
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