September 2013: 3DEM Deposition Rate, Journal Policies

The use of 3D cryo-electron microscopy reconstruction (3DEM) methods to experimentally determine structures of biological macromolecules, complexes and machines is rapidly increasing in the structural biology community. For journal articles reporting new 3DEM structures via single particle, helical, electron crystallography, and sub-tomogram averaging methods, we find that the overall map-deposition rate to EM Data Bank (EMDB) is approaching 70%. However, the rate varies significantly per journal, and tends to be highest for journals with well-defined and consistently enforced 3DEM deposition policies in place (see graph).

We have developed a recommended policy for journals for deposition of 3DEM structural data, including maps to EMDB, and atomic models fitted to maps to PDB, prepared in consultation with the 3DEM community. Mandatory deposition, with release on publication, is recommended for maps representing average structures as well as any fitted atomic models; deposition of representative maps from electron tomography studies is also encouraged.

We have also directly contacted the editors of the journals listed in the graph with recommended updates to their deposition policies. 3DEM community members can further help by recommending deposition in journal referee reports and other editorial correspondence.

Our collaborative project manages the EMDB archive and develops deposition, retrieval, and validation methods for 3DEM data in EMDB and PDB, serving both the 3DEM and the wider scientific communities (doi:10.1093/nar/gkq880). Visit our deposit page to access joint EMDB/PDB deposition services. EMDB and PDB are jointly distributed via the ftp sites of the Worldwide PDB organization which are updated weekly on Wednesdays at 0:00 UTC. The archives presently contain more than 2000 map volumes in EMDB and 600 3DEM-derived atomic models in PDB.