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Deposition Statistics

In the third quarter of 2025, 5478 experimentally-determined structures were deposited to the PDB archive for a total of 16014 entries deposited in the year. Data are processed by wwPDB partners RCSB PDB, PDBe, PDBj and PDBc.

Of the structures deposited in 2025 so far, 85.2% were deposited with a release status of hold until publication  8.2% were released as soon as annotation of the entry was complete  and 6.7% were held until a particular date. 55.4% of these entries were determined by X-ray crystallographic methods  1.3% were determined by NMR methods  and 43.0% by 3DEM.

During the same time quarter, 4227 structures were released in the PDB, including 246 SARS-CoV-2 structures. 2810 EMDB maps were released in the archive.

wwPDB News:

wwPDB Papers Published: IHM and 3DEM Developments

PDB-IHM

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

From PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures determined by integrative/hybrid methods (IHM) are archived alongside experimental structures in PDB as PDB-IHM. These structures are processed by PDB-IHM in parallel to the wwPDB OneDep system and disseminated synchronously with PDB. Integrative structures are assigned PDB accession codes and digital object identifiers.

Integrative ystructures can be accessed from the PDB archive, the PDB-IHM website, and RCSB.org. Read more:

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures
Brinda Vallat, Benjamin M. Webb, Arthur Zalevsky, Hongsuda Tangmunarunkit, Monica R. Sekharan, Serban Voinea, Aref Shafaeibejestan, Jared Sagendorf, Jeffrey C. Hoch, Genji Kurisu, Kyle L. Morris, Sameer Velankar, Carl Kesselman, Stephen K. Burley, Helen M. Berman, Andrej Sali
(2025) Journal of Molecular Biology 437: 168963
10.1016/j.jmb.2025.168963

3DEM Structure-Map Validation Recommendations

Examples of Q-score application in proteins and in nucleic acids adapted from: doi: 10.1107/S2059798325005923

Examples of Q-score application in proteins and in nucleic acids adapted from: doi: 10.1107/S2059798325005923

A new publication describes two percentile-based metrics: Q_relative_all and Q_relative_resolution. The publication presents a statistical analysis of Q-score and these new percentile based validation metrics.

Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
Grigore Pintilie, Chenghua Shao, Zhe Wang, Brian P Hudson, Justin W Flatt, Michael F Schmid, Kyle L Morris, Stephen K Burley, Wah Chiu (2025)
Acta Cryst D81: 410-422
doi: 10.1107/S2059798325005923

Prepare Depositions Using pdb_extract

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pdb_extract is used to extract information from the output files produced by many software for structure determination and to generate a complete PDBx/mmCIF data file ready for PDB deposition

pdb_extract is a pre-deposition service for preparing reusable metadata file and/or structure model files in PDBx/mmCIF format for efficient multiple depositions via wwPDB OneDep deposition.

pdb_extract merges coordinate data, author-provided metadata, and data processing information from output files produced by structure determination programs into a complete PDBx/mmCIF file that can used for easy deposition with OneDep. Use the pdb_extract online form or the easily-installed command line interface (Python).

Depositors are encouraged to use method-specific metadata templates (X-Ray,EM,NMR) to prepare a re-usable common metadata file in PDBx/mmCIF format. This metadata file can then be uploaded to OneDep directly for map-only 3DEM depositions or be merged with coordinate file using pdb_extract for OneDep deposition.

Recent Improvements

  • Log parsing from major XFEL programs CrystFEL and cctbx.xfel
  • Log parsing from refinement programs Phenix and Refmac
  • Generation of a OneDep deposition readiness report
  • Option to download a metadata-only file as a template for related structures
  • Option to download a map-only-metadata file for related 3DEM map-only depositions

Easily Prepare Common Metadata

Depositors are encouraged to use the PDBj CIF editor to easily edit a template file to include corresponding metadata (sequence, crystallization condition, etc.). Method-specific templates have been pre-loaded into the PDBj CIF editor (X-ray, 3DEM, and NMR). Click on the top-left menu (light gray widget icon) to save the edited metadata file in PDBx/mmCIF. Upload this completed file in pdb_extract to prepare single or multiple related structures for submission.