Electron Microscopy Data Bank

Electron Microscopy Data Bank
Name	Electron Microscopy Data Bank
Established	2002
Type	Scientific data repository
Discipline	Structural biology
Location	United Kingdom
Parent	Worldwide Protein Data Bank

Contents

Electron Microscopy Data Bank

The Electron Microscopy Data Bank is an international archival resource for three-dimensional electron microscopy maps and related metadata, providing public access to cryo-electron microscopy and electron tomography datasets used by researchers at institutions such as MRC Laboratory of Molecular Biology, National Institutes of Health, European Molecular Biology Laboratory, California Institute of Technology, and Max Planck Society. It supports deposition practices adopted by initiatives including Worldwide Protein Data Bank, Protein Data Bank in Europe and RCSB Protein Data Bank, and its records are widely cited in publications from journals such as Nature, Science, Cell, PNAS, and EMBO Journal.

History

The archive was initiated in response to community recommendations from meetings sponsored by organizations such as International Union of Crystallography, EM Data Bank Consortium, and funding agencies including Wellcome Trust and National Science Foundation, paralleling developments at Brookhaven National Laboratory and European Synchrotron Radiation Facility. Early milestones involved collaborations with groups at University of Cambridge, Yale University, and University of California, San Francisco to standardize map formats and metadata schemas influenced by practices at Protein Data Bank. Major expansions coincided with technological shifts driven by work from teams led by researchers affiliated with Howard Hughes Medical Institute, Columbia University, and University of Oxford that enabled high-resolution cryo-EM structures deposited after landmark studies cited alongside awards such as the Nobel Prize in Chemistry.

The repository stores cryo-electron microscopy maps, electron tomography volumes, half-maps, masks, and associated metadata reported by laboratories at EMBL-EBI, National Center for Biotechnology Information, Cold Spring Harbor Laboratory, Johns Hopkins University, and University of California, Berkeley. Its holdings cover structures of macromolecular complexes studied by groups at Rockefeller University, MIT, Tokyo Institute of Technology, and Seoul National University, including viral assemblies referenced in publications from Centers for Disease Control and Prevention, ribosomes examined by teams at ETH Zurich, and membrane proteins investigated at University of British Columbia. The database interlinks with model coordinates from deposits to RCSB Protein Data Bank, PDBe, and PDBj and tracks methodological metadata influenced by standards from FAIRsharing and initiatives led by International Workshop on Biomolecular EM.

Depositors from laboratories such as Stanford University, Princeton University, University of Chicago, and University of Toronto follow submission pipelines coordinated with staff from PDBe and RCSB that require map upload, processing metadata, and validation reports. The protocol references file formats and conventions adopted by projects at Electron Microscopy Public Image Archive and tools developed by groups at University of Michigan, University of California, San Diego, and University College London. Submission workflows incorporate validation steps influenced by methods from teams at University of Pennsylvania, University of Washington, and Duke University and align with journal policies from publishers including Springer Nature, Cell Press, and Oxford University Press.

Users at institutions such as Harvard University, Imperial College London, University of Edinburgh, and University of Melbourne access datasets via web portals and programmatic APIs maintained in coordination with EMBL-EBI, RCSB, and PDBe. Search and visualization integrate software from groups at University of Toronto and University of California, San Francisco and leverage viewer technologies developed by teams at University of Illinois Urbana-Champaign and University of Basel. Access patterns reflect usage in consortia including Cryo-EM Network and training programs run by Biophysical Society and Gordon Research Conferences.

The archive interoperates with resources and standards stewarded by Worldwide Protein Data Bank, PDBj, PDBe, and the Electron Microscopy Public Image Archive, and aligns metadata models influenced by committees at International Union of Crystallography and FAIRsharing. Cross-referencing enables linkage to sequence resources at UniProt, functional annotations from Gene Ontology, and literature indexed by PubMed and curated by teams at National Center for Biotechnology Information. Standards development has involved stakeholders from Wellcome Sanger Institute, European Bioinformatics Institute, and Japanese Society for Bioinformatics.

Governance is exercised through consortium arrangements involving EMBL-EBI, RCSB, PDBe, and contributing institutions such as Max Planck Society and Cold Spring Harbor Laboratory, with curation policies informed by committees that include representatives from International Union of Crystallography and funders like Wellcome Trust and NIH. Quality control workflows draw on validation algorithms developed by teams at University of Cambridge, Yale University, and University of California, San Francisco and adopt community standards promoted at meetings like the EM Data Bank Workshop and publications in Nature Methods.

The repository underpins structural studies by laboratories at Rockefeller University, Scripps Research Institute, Harvard Medical School, and Johns Hopkins University, enabling breakthroughs in understanding viral architecture cited in work by Centers for Disease Control and Prevention and antiviral research at NIH. Its datasets have facilitated drug-design efforts reported from Pfizer, Moderna, and AstraZeneca collaborations, and supported methodological advances from groups at University of Oxford, ETH Zurich, and Columbia University. Training and reproducibility efforts by organizations such as Gordon Research Conferences and Biophysical Society routinely use deposits to benchmark algorithms and validate models used in translational research at Mayo Clinic and Cleveland Clinic.

Category:Biological databases