Structures · Database
EMDB
A public repository of cryo-EM density maps and tomograms of macromolecular complexes and subcellular structures.
What EMDB is
The Electron Microscopy Data Bank (EMDB) is a public archive for three-dimensional cryogenic electron microscopy (cryo-EM) density maps, representative tomograms, and associated experimental metadata. It stores structural data spanning macromolecular complexes through to subcellular assemblies.
The repository encompasses reconstructions obtained via single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, and electron crystallography. Hosted as part of EMBL-EBI data resources, EMDB entries provide structural data utilised by researchers and computational platforms such as AlphaFold, cryoSPARC, and modelAngelo.
How it is organised
EMDB accepts depositions of cryo-EM volumes and representative tomograms alongside their experimental parameters. Depositions can be made to the wwPDB directly from structure determination software packages.
Entries in the archive can be queried through text and advanced searches or examined via interactive graphical distributions. The portal indexes records according to sample type, source organism, reconstruction method, resolution, processing software, microscope model, electron source, detector type, and biological classifications such as cellular location and molecular function.
Key facts
- Total entries
- 63259 entries (as of 14 October 2026)
- Data held
- Cryo-EM density maps, representative tomograms, and metadata
- Structural scope
- Macromolecular complexes and subcellular structures
- Supported methods
- Single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, electron crystallography
- Host
- EMBL-EBI
What you can use it for
- Accessing 3D cryo-EM density maps
- Retrieving experimental reconstructed volumes and representative tomograms for structural analysis of macromolecular complexes.
- Analysing structural metadata and instrumentation
- Filtering and comparing experimental datasets by resolution, electron microscope, detector model, and software packages used.
- Evaluating structural models
- Inspecting validation analyses and comparing map entries across macromolecular systems.
- Supporting computational method development
- Providing volume data and metadata to inform and train structure prediction and determination algorithms.
Query it here
The research agent queries EMDB directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Covers multiple cryo-EM reconstruction paradigms, from single-particle analysis to tomography and electron crystallography.
- Facilitates deposition directly from structure determination software packages into the wwPDB.
- Provides interactive navigation and data exploration tools such as Chart builder and entry comparison features.
- Indexes detailed experimental parameters including microscope hardware, detector models, and processing software.
Questions
Can I search EMDB without writing code?
Yes. The research agent queries EMDB directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from EMDB?
CC0 1.0. Terms: https://www.ebi.ac.uk/emdb/about
What types of structures are stored in EMDB?
EMDB stores cryogenic electron microscopy density maps, representative tomograms, and their metadata for macromolecular complexes and subcellular structures.
Which electron microscopy techniques are included?
The database contains entries from single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, and electron crystallography.
How are structures deposited to EMDB?
Data can be deposited to the wwPDB directly through integrated structure determination software packages.
What tools are available for exploring EMDB data?
The database provides an interactive Chart builder tool, comparison views, validation analyses, and search filters covering sample type, organism, method, and hardware configurations.
How to cite it
Fonseca N et al. (2026) Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank. Front. Bioinform. doi: 10.3389/fbinf.2026.1763403
Written from EMDB's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.