EM Data Bank to join the PDB archive

The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, will join the PDB archive (ftp://ftp.wwpdb.org) on 7 March 2012.

The merger marks an important milestone in the Worldwide Protein Data Bank's mission to maintain a single public archive of macromolecular structural data from all structure determination methods that is freely available to the global community. The PDB currently has over 77000 coordinate entries, nearly all with associated experimental data, including 57000 X-ray entries with structure factor files and 6400 NMR entries with restraints. The merger will join all 3DEM results into a single archive, including over 1100 electron microscopy derived maps currently held in EMDB with coordinates for 400 EM map-derived models in PDB, and is an essential step in the wwPDB's development of a Common Deposition & Annotation Tool that will cover all experimental methods, including hybrid methods.

With the addition of EMDB data, the physical size of the complete wwPDB archive will jump from its current 130 GB to roughly 180 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. However, 3DEM depositors will not be directly affected--map and model deposition sessions should continue to be initiated from EMDataBank. All 3DEM map depositions will continue to receive EMDB IDs and all 3DEM coordinate entries will continue to receive PDB IDs.

The Worldwide Protein Data Bank partners are organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006.

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.

Summary information regarding the merger and detailed specifications for data access will be posted here as it becomes available.

25 January 2012 update: The planned wwPDB ftp locations for EMDB map data after 7 March 2012 have changed. Please see the updated links below:

EMDB ftp Access: