333 new PDB entries have been released on 2026-06-10. 254917 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.

Support for the rsync protocol for PDB's Versioned and NextGen archives at RCSB PDB will be discontinued starting June 22. PDBj will continue to support rsync for these archives at: - rsync://rsync-versioned.pdbj.org - rsync://rsync-nextgen.pdbj.org ...

We will be holding a luncheon seminar at the 26th Annual Meeting of the Protein Science Society of Japan on 19 June, 2026. Online participation via Zoom is also available! Seminar title Are you ready for the New PDB Beta Archive and Extended PDB IDs? ...

On July 21, 2027, the wwPDB will fully transition to extended 12-character PDB IDs, the PDBx/mmCIF format, and the re-organized PDB archive. At this point, new 4-character IDs will no longer be issued. PDB Digital Object Identifiers (DOI) can be used to ...

Starting July 21, 2027: - The PDB Beta Archive will replace the current PDB main archive. The current beta archive URL will point to the main archive. - PDB entries that have been issued 4-character PDB IDs, including IHM structures in PDB-IHM, will be ...

All validation reports for released PDB and EMDB entries have been updated and are now available with recalculated percentiles. In addition, validation reports now include new percentile statistics reflecting the state of the PDB archive on December 31, ...

PDBj Newsletter Vol.26 has been released. It outlines our activities for the 2025 fiscal year (from Apr 2025 to Mar 2026).

Newsletter Latest (Vol.26, 6 pages) - 日本語 English Previous news letters are here. Flyer for researchers (2 pages) - 日本語 English Leaflet for general people - 日本語 (A3 6 pages A4 12 pages) 2021 Calendar for celebrating 50th anniversary of PDB ...

- Vol.26 (March 2026) English (pdf 3.0M) / Japanese (pdf 3.9M) - Vol.25 (March 2025) English (pdf 2.9M) / Japanese (pdf 3.2M) - Vol.24 (March 2024) English (pdf 2.9M) / Japanese (pdf 2.9M) - Vol.23 (March 2023) English (pdf 2.7M) / Japanese (pdf 3.0M) - ...

Advancing the Frontiers of Structural Biology The Critical Assessment of Structure Prediction (CASP) experiments, held biennially, have recently witnessed a revolution in modeling accuracy driven by deep learning. In 2018, for the first time, the folds ...

This is the PDBj portal page for PubChem entries linking them with the structures in the PDB archive. The PDBj PubChem Portal enables interactive exploration of protein-ligand interactions by integrating chemical data from PubChem with 3D protein ...

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 ...

EMDB released entry growth by year 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 ...

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 ...

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. ...

Number of PDB depositions per year wwPDB is proud to announce that it surpassed the milestone of 20,000 new structure depositions this year. This achievement reflects the impact of rapid advances in cryo-electron microscopy, high-throughput ...

Congratulations to biocurator Dr. Deborah Harrus on processing over 10,000 PDB depositions. She is the first biocurator at PDBe to reach this milestone and the eighth within the wwPDB. Dr. Harrus joined the Protein Data Bank in Europe (PDBe) in 2019, ...

Starting early January 2026, PDBj will biocurate data depositions coming from Oceania in addition to depositions from other regions in Asia except China. PDBc, an Associate Member of the wwPDB, is responsible for biocurating depositions from China. ...

Metal-protein interaction annotation and metal coordination annotation and assessment Metalloproteins represent ~30% of the PDB archive. Ensuring FAIR data practices for metalloproteins is highly impactful. wwPDB will update existing polyatomic metal ...

The wwPDB is continuing to improve and expand our validation offerings with a new addition to the wwPDB PDF validation reports. Building on the success of the coordinate‑model percentile sliders, which help depositors, reviewers, and archive users assess ...

wwPDB strongly encourages all users to adopt the extended PDB ID format and transition to PDBx/mmCIF file format as soon as possible. This includes making changes to software; referring to structures by the full 12-character ID in all communications; and ...

The EMDB archive is experiencing near-exponential growth. To support this rapid expansion, the wwPDB has been working to prepare our systems for the future and ensure seamless deposition, validation, and dissemination of data in the years ahead. As part ...

Snapshots of the PDB Core archive (https://files.rcsb.org) can be downloaded via HTTPS, SYNC, RSYNC, or FTP. At RCSB PDB, AWS SYNC is supported instead of RSYNC. Snapshots have been archived annually since 2005 to provide readily identifiable data sets ...

Now, we have released the PDBj Newsletter Vol.25.