| [wwPDB] New PDB Beta Archive Available for Testing 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 ... |
| 308 new PDB entries have been released on 2026-02-11. 308 new PDB entries have been released on 2026-02-11. 248942 entries are now available in total. Please refer to PDB / EMDB latest information for other updates. |
| [wwPDB] EMDB Surpasses 10,000 Entries in a Year 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 ... |
| [wwPDB] wwPDB Shared Responsibilities on Data Processing 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 ... |
| [wwPDB] Time-stamped Copies of PDB and EMDB Archives 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. ... |
| [wwPDB] 20,000 Structures Deposited to the PDB in 2025 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 ... |
| [wwPDB] Biocurator Milestone: >10,000 Depositions Processed 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, ... |
| [wwPDB] Coming soon: wwPDB Data Processing Distribution Changes 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. ... |
| [wwPDB] Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs 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 ... |
| [wwPDB] Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report 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] Transitioning to PDBx/mmCIF and Extended PDB IDs 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 ... |
| [wwPDB] Extension to EMDB Accession Codes 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 ... |
| [wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP 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 ... |
| Announcement of the PDBj Newsletter Vol.25 release Now, we have released the PDBj Newsletter Vol.25. |
| Newsletter / Public Relations Resources Newsletter Latest (Vol.25, 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 ... |
| Newsletter - 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) - Vol.22 No.2 (March 2022) English (pdf 2.4M) / Japanese (pdf 2.6M) ... |
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| [wwPDB] Poster Prize Awarded at The Biophysical Society Meeting The wwPDB Foundation made an award for an outstanding student presentation at the 2025 Biophysical Society Meeting (February 15-19, Los Angeles, CA). Hsiang-Ling Huang Mechanisms of dysferlin-mediated membrane repair in health and disease Hsiang- ... |
| [wwPDB] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models We are pleased to announce the release of updated validation reports (version 2) for structures determined using integrative and ... |
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| [wwPDB] PDB-Dev now PDB-IHM Integrative structures are available at wwPDB.org and the PDB archive Structures of many large macromolecular assemblies are now being determined using integrative approaches, wherein information derived from multiple experimental and computational ... |
| [wwPDB] Time-stamped Copies of PDB and EMDB Archives New archive snapshots are available. A snapshot of the PDB Core archive (https://files.wwpdb.org/, https://s3.rcsb.org) as of January 1, 2025 has been added to https://s3snapshots.rcsb.org/, snapshots.rcsb.org (rsync -rlpy -a -v --delete snapshots. ... |
| [wwPDB] Access SDF/MOL formatted CCD files from the PDB archive PDB Chemical Component Dictionary (CCD) files with ideal geometries are now provided in SDF/MOL format at the PDB archive. Users can download individual CCD files in SDF/MOL format from the PDB archive at https://files.wwpdb.org/pub/pdb/refdata/chem_comp/. ... |
| PDBj UniProt Portal This is the PDBj portal page for UniProt entries linking them with the structures in the PDB archive. The portal page provides an overview of the available PDB structures for a PDB entry, ranking them based on resolution and coverage. The UniProt ... |
| A new portal integrating genome variants and protein structures has released A new portal site that connects Japanese gene mutation information published in PDBj with protein sequences and structures (e.g., UniProt ID: P20813) The Protein Data Bank Japan (PDBj, head Prof. Genji Kurisu)*1, operated by the Institute for Protein ... |
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248942
PDB entries from 2026-02-11
