EMDB

EMDB, the Electron Microscopy Data Bank, is a public repository for three-dimensional density maps derived from electron microscopy, including cryo-electron microscopy and related techniques such as negative-stain EM and electron tomography. It archives single-particle reconstructions, tomographic volumes, and other 3D maps, along with extensive metadata describing samples, methods, and instrumentation. Each entry is assigned a unique accession code, typically starting with EMD- followed by a number.

Entries in EMDB include maps used to determine or interpret macromolecular structures. When a corresponding atomic model exists, it can be deposited in the Protein Data Bank or related formats and linked to the EMDB entry, enabling integrated data retrieval of both maps and models. The database supports maps in standard formats such as MRC/CCP4 and stores metadata such as resolution estimates, voxel size, symmetry, imaging technique, specimen description, and publication details.

EMDB is maintained by dedicated teams and operates in coordination with other major structural biology data resources, notably the Protein Data Bank (PDB) family, with metadata standards and deposition workflows designed to enable data sharing and reproducibility.

Access to EMDB is open and its maps are searchable via a web interface and programmatic services. Researchers use EMDB entries for structural interpretation, method development, and validation of electron microscopy-derived models. The resource is widely cited in structural biology and supports ongoing advances in cryo-EM and related methods.