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.
Highlights
Electron cryo-microscopy has very recently become a mainstream area of structural biology and medicine, enabling 3D visualization of a wide variety of biologically important complexes that were previously inaccessible to science
In 2006, scientists in the UK (EMDB) and USA [Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI)] initiated a collaboration funded by National Institutes of Health (NIH) aimed to ensure that data archiving and validation standards for cryo-electron microscopy (EM) maps and models would be coordinated internationally
Results described in Journal of Structural Biology special issue
Summary
Electron cryo-microscopy (cryo-EM) has very recently become a mainstream area of structural biology and medicine, enabling 3D visualization of a wide variety of biologically important complexes that were previously inaccessible to science. The archiving systems and underlying data standards supporting deposition, annotation, release, and validation of cryo-EM structures and the associated metadata describing cryo-EM experiments have been developed over time to support this growth.. Similar to BioMagResBank (BMRB), which archives experimental data from NMR, the EMDB accepts maps determined using any cryo-EM method, including single particle reconstruction with any symmetry, helical filament reconstruction, subtomogram averaging, tomography, and electron crystallography, along with metadata describing the full experimental workflow (Fig. 3). In 2006, scientists in the UK (EMDB) and USA [Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI)] initiated a collaboration funded by National Institutes of Health (NIH) aimed to ensure that data archiving and validation standards for cryo-EM maps and models would be coordinated internationally.. EMDep, designed and implemented at EBI, was the first system designed to collect and annotate maps and associated metadata for EMDB. In 2008, the EMDR team created a joint mapþmodel deposition system for cryo-EM structures by connecting EMDep with
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