About EMDB

Meet the team

The Electron Microscopy Data Bank (EMDB) team operates out of EMBL-EBI and you can read more about us here.

EMDB history

The EMDB is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, 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.

EMPIAR (Electron Microscopy Public Image Archive) is a companion archive to EMDB, founded at and operated by EMBL-EBI, and with a mirror site at PDBj.

Citing EMDB

Please cite the following publication in your papers and on websites: The wwPDB Consortium, EMDB—the Electron Microscopy Data Bank, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D456–D465, https://doi.org/10.1093/nar/gkad1019

To cite individual entries, please quote the EMDB accession code(s) and cite the original publication(s) in which the entries are described.

EMDB logos and branding should not be used on public-facing websites unless explicit prior permission has been obtained from us. However, if you want to use an EMDB logo in a presentation or report, you can use the images in the following table royalty-free and without the need to obtain prior permission from us.

EMDB logo with text in white font (1050 px by 318 px, transparent background)
EMDB logo with text in black font (1050 px by 318 px, transparent background)
EMDB logo without text (219 px by 261 px, transparent background)

More information

Please see our FAQ, Policies, description of the EMDB data model, or contact the EMDB helpdesk.

Funding

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.