wwPDB 2025 News

01/21/2025

Announcing the New PDBx/mmCIF User Guide - Copy

Benefits of the PDBx/mmCIF ecosystem

We are excited to announce the launch of a detailed PDBx/mmCIF File Format User Guide.

As the foundation for depositing, annotating, and archiving structural data across diverse experimental techniques, the Protein Data Bank Exchange macromolecular Crystallographic Information Framework (PDBx/mmCIF) stands as the master format of the Protein Data Bank. Our user-friendly guide offers detailed explanation and examples of essential PDBx/mmCIF records, aimed to facilitate a smooth transition to this format for depositors and users alike.

The wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which 12-character PDB IDs will be issued. Entries with extended PDB IDs will not be compatible with the legacy PDB file format and will only be available in PDBx/mmCIF format. wwPDB encourages users to transition to the PDBx/mmCIF format as soon as possible.

Example PDBx/mmCIF record of a 12-character PDB ID

We invite all users to participate in a brief survey (accessible from the PDBx/mmCIF File Format User Guide) to share feedback on this guide by December 15, 2024. Your feedback will greatly contribute to future developments.

01/16/2025

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 methods is combined to compute their three-dimensional structures. PDB-IHM (formerly PDB-Dev) is a system for archiving and disseminating structures determined using integrative or hybrid methods (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR).

In August 2024, PDB-Dev was unified with the PDB to deliver integrative structures alongside experimental structures in the PDB archive. With unification, integrative structures are assigned PDB accession codes and Digital Object Identifiers (DOIs), annotated as IHM structures, and can be accessed from the PDB archive, PDB DOI links (e.g., DOI: 10.2210/pdb8zzc/pdb), and the PDB-IHM website. Now part of the PDB infrastructure, PDB-Dev has been rebranded as PDB-IHM, denoting IHM structures archived in the PDB.

Integrative structures can be deposited through the PDB-IHM deposition portal and accessible from the wwPDB OneDep home page. They are processed in parallel to the wwPDB OneDep system. Structures processed by PDB-IHM are released synchronously with PDB structures weekly on Wednesdays at 00:00 UTC.

In the future, the wwPDB partners, including Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) in the United States, Protein Data Bank in Europe (PDBe), and Protein Data Bank Japan (PDBj), will disseminate integrative structures on their respective websites.

We look forward to supporting the structural biology community with depositing integrative structures to PDB-IHM.

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

01/05/2025

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.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 20250101 includes the 229,564 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 1,437 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 01, 2025 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20250101/ and ftp://snapshots.pdbj.org/20250101/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (41,367 and 301, respectively) and is 21 TB in size.