The Electron Microscopy Data Bank (EMDB) is a public repository for electron cryo-microscopy volume maps and tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron crystallography (for more information, see the EMDB Policies).
EMDB was founded at EMBL-EBI in 2002 under the leadership of Kim Henrick. From 2007, the archive has been operated jointly by EMBL-EBI and the Research Collaboratory for Structural Bioinformatics (RCSB)a. In 2013, the Protein Data Bank Japan (PDBj) also became involved in EMDB. As of the first of January, 2021, EMDB is an archive operated under the aegis of the Worldwide Protein Data Bank (wwPDB), and has also joined that organisation as a full member.
Results of cryo-EM studies are archived in three collaborating archives:
- EMDB stores the processed 3D volumes and tomograms;
- PDB stores any atomic models that have been constructed based on EMDB data;
- EMPIAR stores the raw EM data underpinning the data in EMDB/PDB.
Data for EMDB and PDB can be deposited through the wwPDB deposition and annotation system OneDep.
Please cite the following publication in your papers and on websites: Lawson CL, Patwardhan A, et al., Berman HM, Kleywegt GJ & Chiu W., “EMDataBank unified data resource for 3DEM.” Nucleic Acids Res. 44, D396-D403 (2016). doi:10.1093/nar/gkv1126. PMID: 26578576; PMCID: PMC4702818.
To cite individual entries, please quote the EMDB accession code(s) and cite the original publication(s) in which the entries are described.
The work on EMDB at EMBL-EBI has been funded in the past by the European Commission, NIH, UKRI-BBSRC and EMBL-EBI (through the EMBL member states). It is currently funded by the Wellcome Trust and EMBL-EBI.
Recent Entries(Show all)
SARS-CoV-2 spike in complex with the S2D106 neutralizing antibody Fab fragment
SARS-CoV-2 spike in complex with the S2D106 neutralizing antibody Fab fragment (local refinement of the RBD and S2D106)
SARS-CoV-2 spike glycoprotein ectodomain in complex with the S2H97 neutralizing antibody Fab fragment
RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)
cryoEM structure of particulate methane monooxygenase associated with Cu(I)
Complex of Bet v 1 with the Fab fragments of a three antibody cocktail
Paired helical filament extracted from PrP-CAA Patient brain tissue
Mouse TRPV3 in MSP2N2 nanodiscs, sensitized state at 42 degrees Celsius
Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees Celsius
Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading
Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody
Cryo-EM structure of vaccine-elicited Rhesus VH6-1 antibody 789-203-3C12 in complex with stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer
In cellulo nuclear pore complex with intermediate diameter from energy depleted S. pombe cells
In cellulo nuclear pore complex in constricted conformation from energy depleted S. pombe cells
M6A and sediment structure inside iron-filled ferritin-M6A without symmetry assumption
Structure of hypercondensed Mumps virus nucleocapsid at 3.6 Angstroms resolution