Community recommendations on cryoEM data archiving and validation

Gerard J Kleywegt¹, Paul D Adams², Sarah J Butcher³, Catherine L Lawson⁴, Alexis Rohou⁵, Peter B Rosenthal⁶, Sriram Subramaniam⁷, Maya Topf⁸, Sanja Abbott¹, Philip R Baldwin⁹, John M Berrisford¹, Gérard Bricogne¹⁰, Preeti Choudhary¹, Tristan I Croll¹¹, Radostin Danev¹², Sai J Ganesan¹³, Timothy Grant¹⁴, Aleksandras Gutmanas¹, Richard Henderson¹⁵, J Bernard Heymann¹⁶, Juha T Huiskonen³, Andrei Istrate¹, Takayuki Kato¹⁷, Gabriel C Lander¹⁸, Shee Mei Lok¹⁹, Steven J Ludtke²⁰, Garib N Murshudov¹⁵, Ryan Pye¹, Grigore D Pintilie²¹, Jane S Richardson²², Carsten Sachse²³, Osman Salih¹, Sjors H W Scheres¹⁵, Gunnar F Schroeder²³, Carlos Oscar S Sorzano²⁴, Scott M Stagg²⁵, Zhe Wang¹, Rangana Warshamanage¹⁵, John D Westbrook⁴, Martyn D Winn²⁶, Jasmine Y Young⁴, Stephen K Burley⁴, Jeffrey C Hoch²⁷, Genji Kurisu¹⁷, Kyle Morris¹, Ardan Patwardhan¹, Sameer Velankar¹

Affiliations

¹ EMBL-EBI, Cambridge, United Kingdom.
² Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ University of Helsinki, Helsinki, Finland.
⁴ RCSB Protein Data Bank, The State University of New Jersey, NJ, USA.
⁵ Genentech, South San Francisco, CA, USA.
⁶ The Francis Crick Institute, London, United Kingdom.
⁷ University of British Columbia, Vancouver, BC, Canada.
⁸ Birkbeck, University of London, London, United Kingdom.
⁹ Salk Institute for Biological Studies, La Jolla, CA, USA.
¹⁰ Global Phasing Limited, Cambridge, United Kingdom.
¹¹ University of Cambridge, Cambridge, United Kingdom.
¹² University of Tokyo, Tokyo, Japan.
¹³ University of California at San Francisco, San Francisco, CA, USA.
¹⁴ Morgridge Institute for Research, Madison, WI, USA.
¹⁵ MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
¹⁶ National Institutes of Health, Bethesda, MD, USA.
¹⁷ Osaka University, Suita, Osaka, Japan.
¹⁸ Scripps Research Institute, La Jolla, CA, USA.
¹⁹ Duke-NUS Medical School, Singapore.
²⁰ Baylor College of Medicine, Houston, TX, USA.
²¹ Stanford University, Stanford, CA, USA.
²² Duke University, Durham, NC, USA.
²³ Forschungszentrum Jülich, Germany.
²⁴ National Center for Biotechnology, Madrid, Spain.
²⁵ Florida State University, Tallahassee, FL, USA.
²⁶ Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom.
²⁷ UConn Health Center, CT, USA.

PMID: 38358351
PMCID: PMC10916293
DOI: 10.1107/S2052252524001246

Community recommendations on cryoEM data archiving and validation

Gerard J Kleywegt et al. IUCrJ. 2024.

. 2024 Mar 1;11(Pt 2):140-151.

doi: 10.1107/S2052252524001246.

Authors

Affiliations

¹ EMBL-EBI, Cambridge, United Kingdom.
² Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ University of Helsinki, Helsinki, Finland.
⁴ RCSB Protein Data Bank, The State University of New Jersey, NJ, USA.
⁵ Genentech, South San Francisco, CA, USA.
⁶ The Francis Crick Institute, London, United Kingdom.
⁷ University of British Columbia, Vancouver, BC, Canada.
⁸ Birkbeck, University of London, London, United Kingdom.
⁹ Salk Institute for Biological Studies, La Jolla, CA, USA.
¹⁰ Global Phasing Limited, Cambridge, United Kingdom.
¹¹ University of Cambridge, Cambridge, United Kingdom.
¹² University of Tokyo, Tokyo, Japan.
¹³ University of California at San Francisco, San Francisco, CA, USA.
¹⁴ Morgridge Institute for Research, Madison, WI, USA.
¹⁵ MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
¹⁶ National Institutes of Health, Bethesda, MD, USA.
¹⁷ Osaka University, Suita, Osaka, Japan.
¹⁸ Scripps Research Institute, La Jolla, CA, USA.
¹⁹ Duke-NUS Medical School, Singapore.
²⁰ Baylor College of Medicine, Houston, TX, USA.
²¹ Stanford University, Stanford, CA, USA.
²² Duke University, Durham, NC, USA.
²³ Forschungszentrum Jülich, Germany.
²⁴ National Center for Biotechnology, Madrid, Spain.
²⁵ Florida State University, Tallahassee, FL, USA.
²⁶ Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom.
²⁷ UConn Health Center, CT, USA.

PMID: 38358351
PMCID: PMC10916293
DOI: 10.1107/S2052252524001246

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.

Keywords: Electron Microscopy Data Bank; Protein Data Bank; bioinformatics; cryogenic-specimen electron microscopy; data archiving; databases; quality control; single-particle cryoEM; structure determination; validation.

open access.

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Figures

**Figure 1**
The ‘resolution revolution’ was largely catalysed by new detector technologies in EM that had particular utility in cryoEM (Kühlbrandt, 2014 ▸). These developments have in subsequent years been bolstered by software developers, instrument manufacturers and the complementary investment of a large part of the scientific workforce utilizing cryoEM. Altogether, this has generated a sustained and approximately logarithmic growth in the number of 3DEM depositions in EMDB (panel a). Further, the technological improvements to the SPA workflow in particular have resulted in a steady increase in the number of 3DEM maps determined and deposited at resolutions sufficient for building an atomic model, in particular <3 and 3–4 Å (panel b). This is further reflected in the number of structures based on cryoEM data deposited in the PDB (panel c). (a) Number of released EMDB entries (on a logarithmic scale) per year (blue) and cumulatively (orange). Data as of December 2023 from https://www.ebi.ac.uk/emdb/statistics/emdb_entries_year. (b) Number of released EMDB entries per year in a number of resolution bins, from 2010 until December 2023 (data from https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_trends_2). (c) Annually released (dark blue) and cumulative (light blue) number of EM-based structures in the PDB as a function of year, from 2010 until December 2023 (data from https://www.rcsb.org/stats/growth/growth-em).

**Figure 2**
Participants in the workshop (not in the photo: S. Abbott and S. J. Ganesan).

See this image and copyright information in PMC

Update of

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.
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. Kleywegt GJ, et al. ArXiv [Preprint]. 2024 Feb 2:arXiv:2311.17640v3. ArXiv. 2024. Update in: IUCrJ. 2024 Mar 1;11(Pt 2):140-151. doi: 10.1107/S2052252524001246. PMID: 38076521 Free PMC article. Updated. Preprint.

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Community recommendations on cryoEM data archiving and validation

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Community recommendations on cryoEM data archiving and validation

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