Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB
Abstract
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.
- Authors:
-
[1];
- SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Stanford Univ., CA (United States)
- SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
- Stanford Univ., CA (United States)
- The State University of New Jersey, Piscataway, NJ (United States)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Lab., Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- Contributing Org.:
- CryoEM & Bioimaging Management
- OSTI Identifier:
- 1772561
- Grant/Contract Number:
- AC02-76SF00515
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 296; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; cryo‐electron microscopy; imaging; single particle analysis; cryo-electron tomography; electron crystallography; protein structure; data archiving
Citation Formats
Chiu, Wah, Schmid, Michael F., Pintilie, Grigore, and Lawson, Catherine L. Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. United States: N. p., 2021.
Web. doi:10.1016/j.jbc.2021.100560.
Chiu, Wah, Schmid, Michael F., Pintilie, Grigore, & Lawson, Catherine L. Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. United States. https://doi.org/10.1016/j.jbc.2021.100560
Chiu, Wah, Schmid, Michael F., Pintilie, Grigore, and Lawson, Catherine L. Mon .
"Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB". United States. https://doi.org/10.1016/j.jbc.2021.100560. https://www.osti.gov/servlets/purl/1772561.
@article{osti_1772561,
title = {Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB},
author = {Chiu, Wah and Schmid, Michael F. and Pintilie, Grigore and Lawson, Catherine L.},
abstractNote = {Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.},
doi = {10.1016/j.jbc.2021.100560},
journal = {Journal of Biological Chemistry},
number = ,
volume = 296,
place = {United States},
year = {Mon Apr 12 00:00:00 EDT 2021},
month = {Mon Apr 12 00:00:00 EDT 2021}
}
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