IUCrJ (Mar 2024)
Community recommendations on cryoEM data archiving 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
Affiliations
- Gerard J. Kleywegt
- EMBL-EBI, Cambridge, United Kingdom
- Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Sarah J. Butcher
- University of Helsinki, Helsinki, Finland
- Catherine L. Lawson
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
- Alexis Rohou
- Genentech, South San Francisco, CA, USA
- Peter B. Rosenthal
- The Francis Crick Institute, London, United Kingdom
- Sriram Subramaniam
- University of British Columbia, Vancouver, BC, Canada
- Maya Topf
- Birkbeck, University of London, London, United Kingdom
- Sanja Abbott
- EMBL-EBI, Cambridge, United Kingdom
- Philip R. Baldwin
- Salk Institute for Biological Studies, La Jolla, CA, USA
- John M. Berrisford
- EMBL-EBI, Cambridge, United Kingdom
- Gérard Bricogne
- Global Phasing Limited, Cambridge, United Kingdom
- Preeti Choudhary
- EMBL-EBI, Cambridge, United Kingdom
- Tristan I. Croll
- University of Cambridge, Cambridge, United Kingdom
- Radostin Danev
- University of Tokyo, Tokyo, Japan
- Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
- Timothy Grant
- Morgridge Institute for Research, Madison, WI, USA
- Aleksandras Gutmanas
- EMBL-EBI, Cambridge, United Kingdom
- Richard Henderson
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- J. Bernard Heymann
- National Institutes of Health, Bethesda, MD, USA
- Juha T. Huiskonen
- University of Helsinki, Helsinki, Finland
- Andrei Istrate
- EMBL-EBI, Cambridge, United Kingdom
- Takayuki Kato
- Osaka University, Suita, Osaka, Japan
- Gabriel C. Lander
- Scripps Research Institute, La Jolla, CA, USA
- Shee-Mei Lok
- Duke-NUS Medical School, Singapore
- Steven J. Ludtke
- Baylor College of Medicine, Houston, TX, USA
- Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
- Grigore D. Pintilie
- Stanford University, Stanford, CA, USA
- Jane S. Richardson
- Duke University, Durham, NC, USA
- Carsten Sachse
- Forschungszentrum Jülich, Germany
- Osman Salih
- EMBL-EBI, Cambridge, United Kingdom
- Sjors H. W. Scheres
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Gunnar F. Schroeder
- Forschungszentrum Jülich, Germany
- Carlos Oscar S. Sorzano
- National Center for Biotechnology, Madrid, Spain
- Scott M. Stagg
- Florida State University, Tallahassee, FL, USA
- Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
- Rangana Warshamanage
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- John D. Westbrook
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
- 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
- Stephen K. Burley
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
- Jeffrey C. Hoch
- UConn Health Center, CT, USA
- Genji Kurisu
- Osaka University, Suita, Osaka, Japan
- Kyle Morris
- EMBL-EBI, Cambridge, United Kingdom
- Ardan Patwardhan
- EMBL-EBI, Cambridge, United Kingdom
- Sameer Velankar
- EMBL-EBI, Cambridge, United Kingdom
- DOI
- https://doi.org/10.1107/S2052252524001246
- Journal volume & issue
-
Vol. 11,
no. 2
pp. 140 – 151
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
- cryogenic-specimen electron microscopy
- data archiving
- validation
- quality control
- electron microscopy data bank
- protein data bank
- single-particle cryoem
- databases
- bioinformatics
- structure determination
