EMDB Database

Overview

The Electron Microscopy Data Bank (EMDB) at EBI archives 3D electron microscopy density maps — primarily cryo-EM and cryo-ET maps — for macromolecular assemblies. It holds 30,000+ entries including ribosomes, membrane proteins, viruses, and large complexes not tractable by X-ray crystallography. The EMDB REST API at https://www.ebi.ac.uk/emdb/api/ provides JSON responses for entry metadata, map download info, fitted atomic models (PDB IDs), and publications. No authentication or API key is required.

When to Use

• Finding cryo-EM density maps for a protein or complex by keyword (e.g., "spike protein", "ribosome 70S")
• Fetching the download URL for a .map.gz density file to use in local structure visualization (UCSF ChimeraX, PyMOL)
• Identifying which PDB atomic models have been fitted into an EMDB map (and vice versa)
• Retrieving EMDB entry metadata — resolution, reconstruction method, fitted model count, and organism — for a literature search or database survey
• Searching for cryo-EM structures of a specific organism or filtered by resolution cutoff (e.g., < 3 Å)
• Linking EMDB maps to their primary publications for citation retrieval
• Use pdb-database instead when you need experimentally determined atomic coordinates (X-ray, NMR, or cryo-EM deposited with coordinates); EMDB provides the raw density map, PDB provides the atom positions
• For AlphaFold AI-predicted structures use alphafold-database-access; EMDB is for experimental EM maps only

Prerequisites