Background

3DEM (Three-Dimensional Electron Microscopy) concerns the use of electron microscopes to determine 3D reconstructions of macromolecules from 2D images. The Electron Microscopy Data Bank (EMDB | emdatabank.org) stores and distributes 3DEM reconstructions. These data, strictly Coloumb potential maps, often inform the modelling of atomic coordinates, whose structures are deposited to the PDB. In addition to atomic coordinates, 3DEM maps encode information about molecular identity, heterogeneity and flexibility. The metadata associated with a 3DEM map can further describe its provenance in terms of sample, preparation, processing and modelling. All together richly describing these data and holding opportunities for data reuse.

Vision

Our vision is that (1) the EMDB archive and prepublication services will support and enrich the scientific record, (2) that FAIR data, metadata and annotations in the EMDB will inform and improve how research is performed and (3) our technology stacks are prepared and can even support future developments in 3DEM.

Data deposition and biocuration

Located in Cambridge, UK at EMBL-EBI, the EMDB is a core member of the wwPDB, which has 5 members: PDBe | EMDB in the UK, RCSB | BMRB in the US, and PDBj in Asia. We work as a coordinated global team to ensure data can be deposited and curated through a common system from anywhere in the world. This deposition and curation system is called OneDep. Data is deposited to teams managing the OneDep system at geographical locations around the world as shown below. For 3DEM experiments this allows the EMDB to receive and release data from across 1,500 institutes, across 77 countries, and 6 continents of the globe.

Impact

The EMDB contains over 47,000 3DEM entries ^ref where over 91% of EMDB entries have been published in approximately 12,000 original scientific publications ^ref predominantly from the UK/EU (37%), North America (34%) and Asia (24%) ^ref. The publications supported by data in the EMDB, have attracted over 510,000 citations in the scientific literature. A publication with supporting data in the EMDB is on average cited 45 times, and the top 10% of most cited publications are cited more than twice that. The most cited publication with supporting data in the EMDB has received over 6,000 citations. [statistics gathered using EMDB and EuropePMC – Jul 2025]

Archive

The exponential productivity of 3DEM methods since the resolution revolution is clearly seen in release statistics of the archive. A technique called single particle analysis dominates these release statistics, as the most commonly employed 3DEM structure determination methodology. Both helical reconstruction and subtomogram averaging are techniques exhibiting similar growth in their use.

Data release

The EMDB @ EMBL-EBI is at its core, a deposition database but also a wwPDB biocuration site and the wwPDB EMDB archive keeper. After data is scheduled for release, normally after peer reviewed publication, data is exchanged by wwPDB biocuration partners around the world for EMDB to prepare that data for public release. This includes but is not limited to preparation for release into a structured FTP, populating data models and databases for public viewing of that data on the website (www.emdatabank.org), adding data annotations to entry data, and making data | metadata available to API’s powering many interfacing systems and external data consumers.

Peer review and validation

The EMDB receives 3DEM data through the OneDep system prior to its publication in the scientific literature. As part of the wwPDB, we are thus uniquely positioned to facilitate the peer review of structural biology research. The EMDB works with software developers in the EM community to evaluate and implement validation tools that help peer reviewers in evaluating maps and models supporting the scientific conclusions of a publication. In general, these tools are evaluated for production readiness and initially implemented as additional validation found on EMDB website entry pages. We then work with the community and wwPDB to move appropriate tools into validation reports where they can support reviewers in the peer review of manuscripts containing 3DEM data.

Data re-use cases

A current and well known data re-use case of structural biology data is AlphaFold. Predicted structures from AlphaFold2 can be explored in the AlphaFold database (https://alphafold.ebi.ac.uk). This was possible because of the free and open access of thousands of model coordinates (PDBs). 

Where these model coordinates have been used to create a paradigm shifting predictive structural biology tool. 3DEM reconstructions in the EMDB encode the information used to infer atomic model coordinates. What would be possible from the re-use of these data?

Did you know 3DEM map data in the EMDB has already been reused to train new algorithms for:

Automated model building in cryoEM (https://doi.org/10.1038/s41586-024-07215-4)

Regularisation of 3DEM reconstructions (https://doi.org/10.1038/s41592-024-02304-8)

At the EMDB we are very interested in enabling methods developers to discover, retrieve and build training datasets to build the next generation of tools in structural biology.

Citing the EMDB

If you find the EMDB useful in your work, or utilise data and resources which we manage, please consider citing the EMDB in your publications:

wwPDB, consortium (November 2023). “EMDB—the Electron Microscopy Data Bank”. Nucleic Acids Research. 52 (D1): D456-465. doi: 10.1093/nar/gkad1019

Contacting the EMDB

For matters related to an EMDB (and associated PDB) deposition made through the OneDep system, please contact us through the OneDep Communication section of your active deposition (monitored daily):

For feedback, praise, or suggestions, please write to us at EMDB through the HelpDesk (monitored weekly):

Alternatively, if you know who you need to contact in the EMDB team, check here.

Related archives

Check out EMPIAR (www.empiar.org)

Check out PDBe (www.pdbe.org)

Funding

The EMDB is funded by:

European Bioinformatics Institute, European Molecular Biology Laboratory (link)

The Wellcome Trust (link)

UKRI (link)

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