EMDB

Info

EMDB is the global public archive of 3D electron microscopy maps of biological specimens. Founded in 2002 at EMBL-EBI (Hinxton, UK). As of 2025, contains >50,000 entries. Became a wwPDB Core Archive in 2021, making the EMDB team a core wwPDB member and the wwPDB-designated Archive Keeper for EMDB.

Key Relationships

• Core Archive of wwPDB (since 2021)
• Located at EMBL-EBI, same campus as PDBe
• Companion archive: EMPIAR (raw EM image data), also at EMBL-EBI with mirror at PDBj
• Depositions managed through wwPDB OneDep system
• Biocuration split geographically: RCSB PDB (Americas/Oceania), PDBe/EMDB team (Europe/Africa), PDBj/PDBc (Asia)
• RCSB PDB also acts as deposition/distribution center under NIH Unified Data Resource for CryoEM
• Software ecosystem: data processed with RELION, cryoSPARC, CCP-EM and others; visualized with ChimeraX, Mol*

People

Name	Role	Affiliation
Kyle Morris	Team Leader, EMDB; wwPDB PI	EMBL-EBI
Ardan Patwardhan	Former lead / correspondence author	EMBL-EBI
Kim Henrick	Founder (2002)	EMBL-EBI (historical)

Funding

• EMBL-EBI core funding (staff, infrastructure)
• Wellcome Trust [212977/Z/18/Z]
• US NIH/NIGMS (R01 GM079429, historical)
• UK MRC/BBSRC (MR/L007835, historical)
• BBSRC (BB/M018423/1)
• EU Framework 7 Programme (284209, historical)

Governance

• Kyle Morris is a wwPDB Principal Investigator
• Sjors Scheres and Giulia Zanetti represent EMDB on the wwPDB Advisory Committee
• EMDB validation tools feed into wwPDB OneDep pipeline
• wwPDB task force-EM Validation oversees validation standards

Key Reference

wwPDB Consortium, NAR 52(D1), D456-D465 (2024). doi:10.1093/nar/gkad1019