Evolving data standards for cryo-EM structures

Lawson, Catherine L.; Berman, Helen M.; Chiu, Wah

doi:10.1063/1.5138589

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:

^[1];

^[2];

^[3]

Rutgers Univ., Piscataway, NJ (United States)
Rutgers Univ., Piscataway, NJ (United States); Univ. of Southern California, Los Angeles, CA (United States)
SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., CA (United States)

Publication Date:: Fri Jan 24 00:00:00 EST 2020

Research Org.:: SLAC National Accelerator Laboratory (SLAC), 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.  doi:10.1063/1.5138589.

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                    Lawson, Catherine L., Berman, Helen M., & Chiu, Wah. Evolving data standards for cryo-EM structures.  United States.  https://doi.org/10.1063/1.5138589

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                    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.

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@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         = {Fri Jan 24 00:00:00 EST 2020},

  month        = {Fri Jan 24 00:00:00 EST 2020}

}

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Title: Evolving data standards for cryo-EM structures

Abstract

Citation Formats

EMDataBank unified data resource for 3DEM journal, November 2015

The Resolution Revolution journal, March 2014

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

CTF Challenge: Result summary journal, June 2015

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

wwPDB biocuration: on the front line of structural biology journal, May 2021

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

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

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

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

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

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

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

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

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

Cryo-electron microscopy shapes up journal, September 2018

EMDB Web Resources journal, March 2018

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

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

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

How Cryo-EM Became so Hot journal, November 2017

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

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

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

The 2010 cryo-em modeling challenge journal, June 2012

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

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing journal, March 1989

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BioMagResBank journal, December 2007

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

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

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

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

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

Outcome of the first electron microscopy validation task force meeting text, January 2012

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

New electron microscopy database and deposition system journal, November 2002

Depositing Electron Microscopy Maps journal, January 2003

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

Anticipating innovations in structural biology journal, January 2018

Cryo-electron microscopy shapes up journal, September 2018

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

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

Mechanism of AAA+ ATPase-mediated RuvAB–Holliday junction branch migration journal, August 2022

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

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

Computed Origami Tomography preprint, January 2020

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

EMDataBank unified data resource for 3DEM
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The Resolution Revolution
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EMDataBank.org: unified data resource for CryoEM
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CTF Challenge: Result summary
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank
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wwPDB biocuration: on the front line of structural biology
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EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information
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EMPIAR: a public archive for raw electron microscopy image data
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Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB
journal, November 2013

The crystallographic information file (CIF): a new standard archive file for crystallography
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
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A 3D cellular context for the macromolecular world
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Outcome of the First Electron Microscopy Validation Task Force Meeting
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A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality
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The first single particle analysis Map Challenge: A summary of the assessments
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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
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The Electron Microscopy eXchange (EMX) initiative
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Cryo-electron microscopy shapes up
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EMDB Web Resources
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Assessing the quality of single particle reconstructions by atomic model building
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EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

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

How Cryo-EM Became so Hot
journal, November 2017

Electron Cryomicroscopy of Biological Machines at Subnanometer Resolution
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Data management challenges in three-dimensional EM
journal, December 2012

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

The 2010 cryo-em modeling challenge
journal, June 2012

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

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing
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Preclinical Development of a Fusion Peptide Conjugate as an HIV Vaccine Immunogen
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BioMagResBank
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Validation of Structures in the Protein Data Bank
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Evaluation system and web infrastructure for the second cryo-EM model challenge
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Comparing cryo-EM structures
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Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution
journal, March 2019

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

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

Outcome of the first electron microscopy validation task force meeting
text, January 2012

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

New electron microscopy database and deposition system
journal, November 2002

Depositing Electron Microscopy Maps
journal, January 2003

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

Anticipating innovations in structural biology
journal, January 2018

Cryo-electron microscopy shapes up
journal, September 2018

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

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

Mechanism of AAA+ ATPase-mediated RuvAB–Holliday junction branch migration
journal, August 2022

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

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

Computed Origami Tomography
preprint, January 2020

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