Data Deposition/Biocuration Services and
Archive Management

In the third quarter of 2024, 4940 experimentally-determined structures were deposited to the PDB archive for a total of 14258 entries deposited in the year.  Data are processed by wwPDB partners RCSB PDB, PDBe, PDBj and PDBc.

Of the structures deposited in 2024 so far, 85.0% were deposited with a release status of hold until publication  9.3% were released as soon as annotation of the entry was complete  and 5.7% were held until a particular date. 56.3% of these entries were determined by X-ray crystallographic methods  1.7% were determined by NMR methods  and 41.8% by 3DEM.

During the same time quarter, 3706 structures were released in the PDB, including 171 SARS-CoV-2 structures. 2228 EMDB maps were released in the archive.

Congratulations to biocurator Dr. Irina Persikova on processing over 10,000 PDB depositions. She is the seventh biocurator in the wwPDB reached this milestone.

Irina has received Ph.D. training in Solid State Physics and provided over 20 years of service to the RCSB PDB. She contributed as an author or co-author to 17 publications and a book chapter.

She has established herself as a highly qualified professional with deep understanding of scientific data and various experimental techniques and dedication to exceptional quality data curation. Her profound data curation expertise and commitment to excellence contributed to the high quality data archive for the benefit of the scientific community. We congratulate Irina with this exciting accomplishment and look forward to her future success.

Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is issued a PDB ID, reported in the PDBx/mmCIF file in the _database_2 category, and “integrative” method provenance is captured at _struct.pdbx_structure_determination_methodology. Users can access and download IHM structures and associated data at files.wwpdb.org/pub/pdb_ihm/.

Currently, holding files in JSON format, validation reports (summary and full reports) in PDF format, and model files in PDBx/mmCIF format are provided.

• /pdb_ihm/holdings/ (current holdings, released structures last modified dates, unreleased entries)
• /pdb_ihm/data/entries/hash/{PDB_id}/validation_reports/ (includes summary and full validation reports)
• /pdb_ihm/data/entries/hash/{PDB_id}/structures/ (latest version of model files)
• For example, https://files.wwpdb.org/pub/pdb_ihm/data/entries/zz/8zz1/structures/8zz1.cif.gz

Data may be expanded in the future based on community needs. In the near future, IHM data will also be available via wwPDB DOI landing pages and wwPDB partner websites.

Questions or feedback? Contact deposit-help@mail.wwpdb.org or pdb-dev@mail.wwpdb.org.

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