Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation

Gerard J Kleywegt; Paul D Adams; Sarah J Butcher; Catherine L Lawson; Alexis Rohou; Peter B Rosenthal; Sriram Subramaniam; Maya Topf; Sanja Abbott; Philip R Baldwin; John M Berrisford; Gérard Bricogne; Preeti Choudhary; Tristan I Croll; Radostin Danev; Sai J Ganesan; Timothy Grant; Aleksandras Gutmanas; Richard Henderson; J Bernard Heymann; Juha T Huiskonen; Andrei Istrate; Takayuki Kato; Gabriel C Lander; Shee-Mei Lok; Steven J Ludtke; Garib N Murshudov; Ryan Pye; Grigore D Pintilie; Jane S Richardson; Carsten Sachse; Osman Salih; Sjors H W Scheres; Gunnar F Schroeder; Carlos Oscar S Sorzano; Scott M Stagg; Zhe Wang; Rangana Warshamanage; John D Westbrook; Martyn D Winn; Jasmine Y Young; Stephen K Burley; Jeffrey C Hoch; Genji Kurisu; Kyle Morris; Ardan Patwardhan; Sameer Velankar

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation

ArXiv [Preprint]. 2024 Feb 2:arXiv:2311.17640v3.

Authors

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, UK.
² Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA.
³ University of Helsinki, Helsinki, Finland.
⁴ RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA.
⁵ Genentech, South San Francisco, California, USA.
⁶ The Francis Crick Institute, London, UK.
⁷ University of British Columbia, Vancouver, BC, Canada.
⁸ Birkbeck, University of London, London, UK.
⁹ The Salk Institute for Biological Studies, La Jolla, CA, USA.
¹⁰ Global Phasing Limited, Cambridge, UK.
¹¹ University of Cambridge, Cambridge, UK.
¹² The 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, UK.
¹⁶ National Institutes of Health, Bethesda, MD, USA.
¹⁷ Osaka University, Suita, Osaka, Japan.
¹⁸ Scripps Research, 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 of Biotechnology (CSIC), Madrid, Spain.
²⁵ Florida State University, Tallahassee, FL, USA.
²⁶ Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK.
²⁷ UConn Health, USA.

PMID: 38076521
PMCID: PMC10705588

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.

Keywords: Cryogenic-specimen Electron Microscopy; Electron Microscopy Data Bank; Protein Data Bank; data archiving; quality control; validation.

Publication types

Preprint

Abstract

Publication types

Grants and funding