wwPDB 2026 News

03/05/2026

PDB Reaches a New Milestone

The PDB contains more than 250,000 entries

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With this week's update, the PDB archive contains a record 250,441 entries.

Established in 1971, this central, public archive has reached this critical milestone thanks to the efforts of structural biologists throughout the world who contribute their experimentally-determined protein and nucleic acid structure data.

wwPDB data centers support online access to three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy.

The wwPDB passed the 200,000 milestone in 2023. More than 20,000 new structure depositions were submitted to the archive in 2025; PDB data were accessed more than 4.7 billion times in the same year.

Function follows form

In the 1950s, scientists had their first direct look at the structures of proteins and DNA at the atomic level. Determination of these early three-dimensional structures by X-ray crystallography ushered in a new era in biology-one driven by the intimate link between form and biological function. As the value of archiving and sharing these data were quickly recognized by the scientific community, the Protein Data Bank (PDB) was established as the first open access digital resource in all of biology by an international collaboration in 1971 with data centers located in the US and the UK.

Among the first structures deposited in the PDB were those of myoglobin and hemoglobin, two oxygen-binding molecules whose structures were elucidated by Chemistry Nobel Laureates John Kendrew and Max Perutz. With this week's regular update, the PDB welcomes 266 new structures into the archive. These structures join others vital to drug discovery, bioinformatics and education.

The PDB is growing rapidly, increasing in size by ~160% since 2011 (doubling in size every 6-8 years). In 2022, an average of 275 new structures were released to the scientific community each week. The resource is accessed hundreds of millions of times annually by researchers, students, and educators intent on exploring how different proteins are related to one another, to clarify fundamental biological mechanisms and discover new medicines.

More than Twenty Years of Collaboration

Since its inception, the PDB has been a community-driven enterprise, evolving into a mission critical international resource for biological research. The wwPDB partnership was established in July 2003 with PDBe, PDBj, and RCSB PDB. Today, the collaboration includes partners BMRB (joined in 2006) and EMDB (2021).

The wwPDB ensures that these valuable atomic coordinate and experimental supporting data are securely stored, expertly managed, and made freely available for the benefit of scientists and educators around the globe. wwPDB data centers work closely with community experts to define deposition and annotation policies, resolve data representation issues, and implement community validation standards. In addition, the wwPDB works to raise the profile of structural biology with increasingly broad audiences.

Each structure submitted to the archive is carefully curated by wwPDB staff before release. New depositions are checked and enhanced with value-added annotations and linked with other important biological data to ensure that atomic coordinate and experimental supporting data are discoverable and interpretable by users with a wide range of backgrounds and interests.

wwPDB eagerly awaits the next 50,000 structures and the invaluable knowledge these new data will bring.

02/10/2026

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, 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.

New PDB beta archive available for testing in support of extended PDB IDs

01/19/2026

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 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.

01/12/2026

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 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

Data processing distribution map

01/11/2026

Register for PDB Workshops at IUCr2026

wwPDB will be part of the Twenty-Seventh Congress and General Assembly of the International Union of Crystallography (IUCr2026) that will be held August 11-18, 2026 in Calgary, Alberta (Canada).

Register now to join the wwPDB for free, half-day and hands-on workshops that will be held just before the Congress begins.

Enhancing PDB Deposition and Validation Practices (afternoon session on Monday, August 10, 2026)

Pre-meeting workshop: OneDep

This workshop will provide participants with essential knowledge and skills to easily prepare PDB depositions, evaluate structure quality, and utilize OneDep features to streamline and optimize deposition processes.

Through short lectures and hands-on practical sessions, participants will gain proficiency in making successful PDB depositions using available tools for preparation of necessary data and metadata files consistent with OneDep requirements of the wwPDB OneDep system for complete deposition, rigorous validation, and expert biocuration. Participants will develop a comprehensive understanding of information presented within wwPDB validation reports and the importance in assessing data quality. Practical insights will be shared, enabling participants to confidently undertake and complete successful PDB submissions.

Workshop attendees will also become proficient in leveraging various features and tools integrated into the structure determination software packages and OneDep software system, including automatic initiation of new depositions using application programming interface (API) or using traditional web interface via ORCiD to create deposition sessions, and validating deposited data.

Enabling PDB Deposition of Integrative/Hybrid Methods Structures Determined using 3D Electron Microscopy plus Chemical Crosslinking and Other Complementary Approaches with the PDB-IHM System (afternoon session on Tuesday, August 11, 2026)

Pre-meeting workshop: IHM Deposition

This workshop will enable structural biologists to learn about the advantages of using the PDB-IHM system to make complete depositions of 3DEM/Xlinking-MS-based IHM structures and other types of integrative structures to the PDB.

Structures of complex macromolecular assemblies are increasingly determined using integrative or hybrid methods (IHM), wherein complementary experimental and computational techniques are employed. In addition to traditional structure determination methods such as macromolecular crystallography, NMR spectroscopy, and three-dimensional electron microscopy (3DEM), complementary techniques (e.g., chemical crosslinking-mass spectrometry (Xlinking-MS), small-angle scattering, Förster resonance energy transfer, and chemical shift perturbation without NOE restraints) frequently contribute to integrative structure determination.

PDB-IHM, part of the PDB Core Archive, enables deposition, validation, biocuration, preservation, and dissemination of IHM structures. PDB-IHM infrastructure is supported by the IHMCIF data standard (an extension of the PDBx/mmCIF data standard underpinning the PDB) and software tools that ensure FAIR (findable, accessible, interoperable, and reusable) availability of integrative structural biology data. Importantly, integrative structures processed through PDB-IHM receive PDB accession codes and are archived alongside “traditional” single-method experimental structures in the PDB.

The primary goal of this workshop is to facilitate deposition of IHM structures using PDB-IHM functionality, thereby eliminating barriers to fully archiving these structures in the PDB and preventing data loss. Given the predominance of combined 3DEM/Xlinking-MS-based integrative structures, the workshop will highlight these use cases. Through a combination of short lectures and hands-on practical sessions, participants will learn about (a) IHM data deposition requirements, standards, and practices, (b) pre-deposition file preparation, (c) deposition process and workflows, (d) depositing structures through the web interface, (e) submitting multiple structures using an API, and (f) interpreting the information presented in wwPDB validation reports.

Visit IUCr 2026 for complete details about this structural science meeting.
Depositors should register for the workshops during the registration process; early registration ends March 31, 2026.

01/07/2026

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.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.