By 2028 4-character PDB IDs (e.g. 1abc) will be fully allocated. After that, all new entries will be assigned only extended PDB IDs.

The new extended PDB ID format will be 12 characters, which includes a prefix pdb_ followed by 8 alphanumeric characters, e.g. pdb_1000axyz. This new ID format will enable text mining detection of PDB entries in the published literature and allow for more informative and transparent delivery of revised data files. When submitting extended PDB IDs to journals and citing extended PDB IDs in manuscripts, all 12 characters including prefix pdb_ should be provided.

A PDB Beta Archive is now available to help community adopt extended PDB ID and PDBx/mmCIF format during the transition phase. All files at this archive are re-organized with extended PDB ID (including file naming and directories) at entry level, mirroring the same data organization of the PDB Versioned Archive.

All data files for a particular entry are stored in a single directory, labeled based on a two-character hash generated from the penultimate two characters of the PDB code, i.e., https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/<two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>. The two-letter hash will be based on the second and third characters from the last character. For example, PDB entry pdb_1abc5678 will be under /67/. This will maintain consistency with the current PDB archive: PDB entry 1abc is under /ab.

File naming is standardized such that the file type is used for the extension.
For example, file naming is changed from r116dsf.ent.gz to pdb_0000116d-sf.cif.gz for the structure factor file and from pdb318d.ent.gz to pdb_0000318d.pdb.gz for the legacy PDB formatted coordinate file.

When four character PDB IDs are about to be consumed, this PDB Beta Archive will replace the current PDB Archive (expect to be around mid-2027) and entries with extended PDB IDs issued are not compatible with PDB format. wwPDB encourages scientific journals, PDB community and users to transition to PDBx/mmCIF format and adopt new PDB ID format as earlier as possible.

For any further information please contact us at info@wwpdb.org.

[ wwPDB News ]

The wwPDB has reached a historic milestone, releasing 10,000 EMDB entries in a single year.

The rate of release of 3DEM data to the public continues at an extraordinary pace, for the first time the wwPDB has seen the release of 10,000 entries from the EMDB in just a single year. To put this in context, in 2019 the EMDB stood at 10,000 entries in total, after 17 years of growth. Now in 2025 due to the current volume of data release, the archive has surpassed 50,000 total entries.

This rapid growth is a testament to the hard work of the community which the wwPDB endeavors to support. It also highlights the ongoing challenge the community is facing with ever more data created requiring streamlined deposition, processing, curation, peer-review, and sustainable & scalable archiving practices. We are excited to continue to be part of structural biology history.

[ wwPDB News ]

Depositions are automatically distributed to wwPDB deposition centers geographically.

Data processing responsibilities are shared among wwPDB partner sites:

• RCSB PDB is responsible for PDB and EMDB data coming from the Americas
• PDBe and EMDB are responsible for PDB and EMDB data from Europe (except Belarus and Russian Federation) and Africa
• PDBj is responsible for PDB and EMDB data from Asia regions (except China), Belarus, Russian Federation and Oceania
• PDBc is responsible for PDB and EMDB data from China
• BMRB is responsible for BMRB data from the Americas, Africa, and Europe
• BMRBj is responsible for BMRB data from Asia

[ wwPDB News ]

A snapshot of the PDB Core archive (https://files.wwpdb.org, https://s3.rcsb.org) as of January 01, 2026 has been added to https://s3snapshots.rcsb.org (AWS), snapshots.rcsb.org (rsync -rlpy -a -v --delete snapshots.rcsb.org:: .), and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20260101 includes the 246,905 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 1,583 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 01, 2026 can be found in https://ftp.ebi.ac.uk/pub/databases/emdb_vault/20260101/ and ftp://snapshots.pdbj.org/20260101/. The snapshot includes 52,943 3DEM entries. The Snapshot of the EMDB archive is 28.2 TB in size.

[ wwPDB News ]