EM Data Bank part of PDB archive

The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, has joined the PDB archive (https://files.wwpdb.org), as announced previously.

The merger makes 3DEM results available in a single archive, including over 1300 electron microscopy derived maps from EMDB and 400 coordinates for EM map-derived models in PDB. It is also an essential step in the wwPDB's development of a Common Deposition & Biocuration Tool that will cover all experimental methods, including hybrid methods.

With the addition of EMDB data, the physical size of the complete wwPDB archive jumps to roughly 180 GB (from its previous 130 GB). Sites that mirror the full wwPDB archive will need to increase storage capacity accordingly.

The main impact for 3DEM data users will be the change in download links for maps:

• https://files.wwpdb.org/pub/emdb
• ftp://ftp.ebi.ac.uk/pub/databases/emdb
• ftp://ftp.pdbj.org/pub/emdb

3DEM depositors will not be affected--map and model deposition sessions will continue at EMDataBank. All 3DEM map depositions will continue to receive EMDB IDs and all 3DEM coordinate entries will continue to receive PDB IDs.

The wwPDB partners are organizations that act as deposition, data processing and distribution centers for PDB data. Members are RCSB PDB (USA), PDBe (Europe) PDBj (Japan), and BMRB (USA).

The EMDB was established in 2002 by PDBe at the European Bioinformatics Institute, and is currently operated by EMDataBank, Unified Data Resource for 3DEM, established in 2007 as a joint effort of PDBe, RCSB PDB, and NCMI. EMDataBank will continue to serve the 3DEM and wider scientific communities with its 3DEM-specific portal for deposition and access to EM-derived structures with links to software, validation standards and conventions.