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314 new PDB entries have been released on 2025-07-09.

314 new PDB entries have been released on 2025-07-09. 238582 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.

[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 Snapshots have been archived annually since 2005 to provide readily identifiable data sets ...

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Staff

- Head KURISU, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - KURISU, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - Group for Data-in of PDB/EMDB Nakagawa, Atsushi, Ph.D. (Prof., IPR, Osaka Univ.) YU, Jian, Ph.D. (Assoc. Prof., IPR, Osaka Univ.) CHO, Hasumi (CHEN, ...

Announcement of the PDBj Newsletter Vol.25 release

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

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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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 ...

[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- ...

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PDB data is freely available for both commercial and non-commercial use (CC0 1.0 Universal Public Domain Dedication). For using other contents in PDBj site, see also the description below for details. You can freely link to any pages in our site ...

PDBj Advisory Committee

Advisors from the Scientific Community - Koga, Nobuyasu (Institute for Protein Research, The University of Osaka) - Mitsuoka, Kaoru (Research Center for Ultra-High Voltage Electron Microscopy, The University of Osaka) - Senda, Toshiya (Institute of ...

[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 ...

How to download from the PDB/snapshot archive

PDB Archive The PDB data sites are updated every Wednesday at 00:00 UTC / 09:00 JST. ( The PDB NextGen Repositories are updated every month on the 1st Wednesday at 00:00 UTC / 09:00 JST.) The latest PDB raw data is available from the PDB Archive ...

[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. ...

BMRB

https://bmrbdep.pdbj.org/index_en.html BMRB (Biological Magnetic Resonance Data Bank) is a database for NMR data of peptides, proteins, and nucleic acids, managed by the BioMagResBank at the University of Connecticut, USA. This website is maintained by ...

[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/. ...

Support Fund for Protein Data Bank Japan

Donation to this project Protein Data Bank Protein Data Bank (PDB), a database that archives the 3D structural information of biomacromolecules determined by experimental methods, started in 1971 with seven entries in the United States. In the latter ...

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

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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 ...

Derived databases

eF-site eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, ...

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PDBj luncheon seminar at APBJC 2024

We will hold a luncheon seminar at APBJC 2024 (1st Asia & Pacific Bioinformatics Joint Conference ~JSBi, GIW, InCoB, APBC, and ISCB-Asia~) on Thursday, October 24, 2024. We look forward to seeing you there. Date 24th October 2024 (Thu) 12:30 - 13:30 ( ...

238582

PDB entries from 2025-07-09

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