Data Deposition/Biocuration Services and Archive Management

In the fourth quarter of 2019, 3070 experimentally-determined structures were deposited to the archive. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

13,377 structures were deposited in 2019. Of all structures deposited this year, 88.0% were deposited with a release status of hold until publication; 7.2% were released as soon as annotation of the entry was complete; and 4.8% were held until a particular date. 82.0% of these entries were determined by X-ray crystallographic methods; 3.0% were determined by NMR methods; and 14.6% by 3DEM.

11,523 new PDB structures were released in 2019. They account for 7.2% of the year-end total holdings of 159,140 available entries.

2,436 EMDB map entries were released in 2019.

wwPDB validation reports now have additional validation for electron microscopy (EM) maps to help users identify potential discrepancies in their data.

The updated reports now incorporate an extensive EM map validation process, integrating a range of established validation methods for EM data previously available at EMDB. This additional EM validation is currently provided to OneDep depositors; it will be provided for entries throughout the PDB and EMDB archives in the future.

The process includes an analysis of the fit of the PDB model to EMDB map, represented at an amino acid level on the residue-property plots and globally by a visual overlay of the map and model. FSC curves are also included to compare reported and estimated resolution, where either half maps or FSC data was uploaded.

Map and Model fitting: top-weak, bottom-good

EM map/model fit as displayed in the new validation reports. The top images display three orthogonal views of the map and model for EMD-0360 and 6N7P and highlight where there are regions of the model not covered by the EM map at the provided contour level. The bottom images show the fit of EMD-9105 and 6ME0, where the majority of the model fits well to the map at the provided contour level.

Included in the reports are images of orthogonal projections, central slices, mask visualization, and more, allowing for inspection of details in the map and identification of artifacts. A statistical analysis of the EM map volume is also provided, including graphs of map density distribution, volume estimate by contour, and rotationally averaged power spectrum.

These changes should help identify potential errors in EM data and provide clarity about potential limitations of the data in both the PDB and EMDB.

Additional information about these validation reports is available at wwPDB.

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

  • Analyze, curate, and validate macromolecular structures from the PDB community
  • Participate in exciting projects with significant impact on the scientific community
  • Communicate daily with members of the research community
  • Participate in fun outreach activities

RCSB PDB provides a friendly working environment and excellent professional development opportunities.  This academic position offers New Jersey state benefits and a faculty-level salary.
For more, visit our Careers page or Contact Us with questions.

RCSB PDB Annotators and Proteomics Building

  • Protein Data Bank: the single global archive for 3D macromolecular structure data
     (2019) Nucleic Acids Research 47: D520–D528. doi:10.1093/nar/gky949
  • Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) (2019) Acta Crystallographica Section D 75: 451-454 doi:10.1107/S2059798319004522
  • Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
    (2019) Structure 27: 1745-1759 doi: 10.1016/j.str.2019.11.002