skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Evolving data standards for cryo-EM structures

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.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]
  1. Rutgers Univ., Piscataway, NJ (United States)
  2. Rutgers Univ., Piscataway, NJ (United States); Univ. of Southern California, Los Angeles, CA (United States)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS)
OSTI Identifier:
1608985
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Structural Dynamics
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2329-7778
Publisher:
American Crystallographic Association/AIP
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Lawson, Catherine L., Berman, Helen M., and Chiu, Wah. Evolving data standards for cryo-EM structures. United States: N. p., 2020. Web. https://doi.org/10.1063/1.5138589.
Lawson, Catherine L., Berman, Helen M., & Chiu, Wah. Evolving data standards for cryo-EM structures. United States. https://doi.org/10.1063/1.5138589
Lawson, Catherine L., Berman, Helen M., and Chiu, Wah. Fri . "Evolving data standards for cryo-EM structures". United States. https://doi.org/10.1063/1.5138589. https://www.osti.gov/servlets/purl/1608985.
@article{osti_1608985,
title = {Evolving data standards for cryo-EM structures},
author = {Lawson, Catherine L. and Berman, Helen M. and Chiu, Wah},
abstractNote = {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.},
doi = {10.1063/1.5138589},
journal = {Structural Dynamics},
number = 1,
volume = 7,
place = {United States},
year = {2020},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

EMDB Web Resources
journal, March 2018

  • Abbott, Sanja; Iudin, Andrii; Korir, Paul K.
  • Current Protocols in Bioinformatics, Vol. 61, Issue 1
  • DOI: 10.1002/cpbi.48

Assessing the quality of single particle reconstructions by atomic model building
journal, November 2018


EMDataBank unified data resource for 3DEM
journal, November 2015

  • Lawson, Catherine L.; Patwardhan, Ardan; Baker, Matthew L.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1126

EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

  • Tang, Guang; Peng, Liwei; Baldwin, Philip R.
  • Journal of Structural Biology, Vol. 157, Issue 1
  • DOI: 10.1016/j.jsb.2006.05.009

Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology
journal, August 2005

  • Heymann, J. Bernard; Chagoyen, Mónica; Belnap, David M.
  • Journal of Structural Biology, Vol. 151, Issue 2
  • DOI: 10.1016/j.jsb.2005.06.001

The Resolution Revolution
journal, March 2014


Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution
journal, March 2000


How Cryo-EM Became so Hot
journal, November 2017


EMDataBank.org: unified data resource for CryoEM
journal, October 2010

  • Lawson, C. L.; Baker, M. L.; Best, C.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq880

New electron microscopy database and deposition system
journal, November 2002


CTF Challenge: Result summary
journal, June 2015

  • Marabini, Roberto; Carragher, Bridget; Chen, Shaoxia
  • Journal of Structural Biology, Vol. 190, Issue 3
  • DOI: 10.1016/j.jsb.2015.04.003

Electron Cryomicroscopy of Biological Machines at Subnanometer Resolution
journal, March 2005


Data management challenges in three-dimensional EM
journal, December 2012

  • Patwardhan, Ardan; Carazo, José-Maria; Carragher, Bridget
  • Nature Structural & Molecular Biology, Vol. 19, Issue 12
  • DOI: 10.1038/nsmb.2426

A New Generation of Crystallographic Validation Tools for the Protein Data Bank
journal, October 2011


EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
journal, August 2015

  • Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3541

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information
journal, October 2003


The 2010 cryo-em modeling challenge
journal, June 2012

  • Ludtke, Steven J.; Lawson, Catherine L.; Kleywegt, Gerard J.
  • Biopolymers, Vol. 97, Issue 9
  • DOI: 10.1002/bip.22081

Web server for tilt-pair validation of single particle maps from electron cryomicroscopy
journal, April 2014


EMPIAR: a public archive for raw electron microscopy image data
journal, March 2016

  • Iudin, Andrii; Korir, Paul K.; Salavert-Torres, José
  • Nature Methods, Vol. 13, Issue 5
  • DOI: 10.1038/nmeth.3806

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB
journal, November 2013

  • Lagerstedt, Ingvar; Moore, William J.; Patwardhan, Ardan
  • Journal of Structural Biology, Vol. 184, Issue 2
  • DOI: 10.1016/j.jsb.2013.09.021

The crystallographic information file (CIF): a new standard archive file for crystallography
journal, November 1991

  • Hall, S. R.; Allen, F. H.; Brown, I. D.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 6
  • DOI: 10.1107/S010876739101067X

Single particle electron cryomicroscopy: trends, issues and future perspective
journal, January 2016


BioMagResBank
journal, December 2007

  • Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm957

Validation of Structures in the Protein Data Bank
journal, December 2017


OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
journal, March 2017


Evaluation system and web infrastructure for the second cryo-EM model challenge
journal, October 2018

  • Kryshtafovych, Andriy; Adams, Paul D.; Lawson, Catherine L.
  • Journal of Structural Biology, Vol. 204, Issue 1
  • DOI: 10.1016/j.jsb.2018.07.006

A 3D cellular context for the macromolecular world
journal, October 2014

  • Patwardhan, Ardan; Ashton, Alun; Brandt, Robert
  • Nature Structural & Molecular Biology, Vol. 21, Issue 10
  • DOI: 10.1038/nsmb.2897

Comparing cryo-EM structures
journal, December 2018


Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution
journal, March 2019

  • Zhang, Kaiming; Zhang, Huawei; Li, Shanshan
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 14
  • DOI: 10.1073/pnas.1821959116

Outcome of the First Electron Microscopy Validation Task Force Meeting
journal, February 2012


A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality
journal, February 2019


Protein Data Bank: the single global archive for 3D macromolecular structure data
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky949

Automatic particle selection: results of a comparative study
journal, January 2004


Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
journal, June 1990


The first single particle analysis Map Challenge: A summary of the assessments
journal, November 2018

  • Heymann, J. Bernard; Marabini, Roberto; Kazemi, Mohsen
  • Journal of Structural Biology, Vol. 204, Issue 2
  • DOI: 10.1016/j.jsb.2018.08.010

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores
journal, December 2018


Bsoft: Image processing and molecular modeling for electron microscopy
journal, January 2007


The Electron Microscopy eXchange (EMX) initiative
journal, May 2016

  • Marabini, Roberto; Ludtke, Steven J.; Murray, Stephen C.
  • Journal of Structural Biology, Vol. 194, Issue 2
  • DOI: 10.1016/j.jsb.2016.02.008

Building bridges between cellular and molecular structural biology
journal, July 2017


Depositing Electron Microscopy Maps
journal, January 2003


Anticipating innovations in structural biology
journal, January 2018

  • Berman, Helen M.; Lawson, Catherine L.; Vallat, Brinda
  • Quarterly Reviews of Biophysics, Vol. 51
  • DOI: 10.1017/S0033583518000057

Cryo-electron microscopy shapes up
journal, September 2018