Data Deposition/Biocuration Services and Archive Management

In the third quarter of 2019, 3327 experimentally-determined structures were deposited to the archive. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

88.1% were deposited with a release status of hold until publication; 7.5% were released as soon as annotation of the entry was complete; and 4.3% were held until a particular date.

82.2% of these entries were determined by X-ray crystallographic methods; 3.1% by NMR methods; and 14.5% by 3DEM.

During the same period, 3060 structures and 865 EMDB maps were released in the PDB.

Depositors can now submit new coordinates for released entries without changing the PDB ID.

PDB versioning is initially limited to entries submitted via OneDep. This functionality will later be extended to entries deposited in legacy systems (ADIT and Autodep).

Versionning requests should be initiated using the OneDep communication panel within the deposition session for the entry in question. Once submitted, the revised model will be processed by wwPDB biocurators and a new version released. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year.

The most recent version of the entry will be available in the main PDB archive FTP (http://ftp.wwpdb.org). All major versions of a PDB structure will be retained in the versioned FTP archive (ftp-versioned.wwpdb.org) - more information can be found on the wwPDB website. The structure of the versioned FTP archive has been built allowing for future extension of the PDB code format. PDB entry 1abc would therefore be found in the folder pdb_00001abc.

Changes made to entries during versioning are considered to be either “major” or “minor”. Updates to atomic coordinates, polymer sequence, or chemical description trigger a major version increment, while changes to any other categories are indicated as “minor”. Changes introduced are recorded in the PDBx/mmCIF audit categories.

If you have any further queries regarding the process of PDB versioning, please contact the wwPDB at deposit-help@mail.wwpdb.org.

RCSB PDB is looking for a Biochemical Information & Annotation Specialist to join the RCSB PDB team at Rutgers, The State University of New Jersey.

Deposition/Biocuration Services support Data Depositors who submit the results of their structural studies of biological macromolecules to the PDB. All data deposited undergo expert review. Each structure is examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources, and validated for scientific/technical accuracy.

Biocurators communicate daily with members of the deposition community, and annotate, publicly release, and update entries in the PDB archive.

For more information, see

wwPDB biocuration supporting open access to high-quality 3D structural biology data (2018) Database 2018: bay002 doi: 10.1093/database/bay002

The rewards of working as a data wrangler Science Careers doi: 10.1126/science.caredit.aaq0481

For more, visit our Careers page or Contact Us with questions.