Yuhe Liang

Through the RCSB.org research-focused web portal, many millions of users access rigorously validated, expertly biocurated, 3D biostructure information stored in the Protein Data Bank (PDB) archive alongside predicted Computed Structure Models (CSMs) from AlphaFold DB and ModelArchive. Specialized tools and related resources, from 3D visualization to protein annotations, allow deep exploration of this rich trove of data. The recently updated RCSB.org Advanced Search interface provides a more intuitive experience with enhanced support for 3D structure exploration. The 3D Similarity Search option is powered by a new AI-based system that is more accurate and scalable to much larger collections of structures. Additional capabilities are provided through web-based APIs and a Python API wrapper package that enable researchers to easily interact with RCSB PDB programmatic services for individually tailored analyses. These resources, together with a statistics tool, training and documentation, and the upcoming wwPDB ID and archive transition, are described.

Motivation: Structural biologists have contributed more than 260 000 experimentally determined three-dimensional structures of biological macromolecules to the Protein Data Bank. Incoming depositions are validated and biocurated by approximately 20 expert biocurators at the collaborating data centers worldwide. Biocurators at the Research Collaboratory for Structural Bioinformatics Protein Data Bank, who process more than 40% of global depositions, face growing difficulty sustaining efficient Help Desk operations, having received roughly 19 000 depositor messages across some 8000 entries in 2025. Results: We developed an artificial intelligence Help Desk assistant built on retrieval-augmented generation. Source documents are converted to Markdown with layout preserved, divided by a two-stage chunking procedure, embedded, and stored in a relational vector database. At query time, maximal marginal relevance retrieval selects diverse supporting passages, a topical guardrail filters out-of-scope questions, and a purpose-built system prompt prevents disclosure of internal curation terminology. Separate language model configurations handle question condensing and answer generation. The service runs in production on a container orchestration platform, providing around-the-clock depositor assistance with streaming, citation-backed responses. Availability and implementation: Freely available at https://rcsb-deposit-help.rcsb.org. Source code: https://github.com/rcsb/rcsb-pdb-helpdesk (archived at Zenodo: https://doi.org/10.5281/zenodo.19560785).

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints. Highlights PDB Structure Validation Report expanded to include Restraint Analysis NMR Exchange Format (NEF) and NMR-STAR for distance restraint representation Standard distance and dihedral restraint formats for model vs. restraint assessment Standardized restraint formats provide interoperability between modeling programs

The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

Endoplasmic reticulum–associated degradation (ERAD) is a protein quality control pathway of fundamental importance to cellular homeostasis. Although multiple ERAD pathways exist for targeting topologically distinct substrates, all pathways require substrate ubiquitination. Here, we characterize a key role for the UBE2G2 BindingRegion (G2BR) of the ERAD accessory protein ancient ubiquitous protein 1 (AUP1) in ERAD pathways. This 27-amino acid (aa) region of AUP1 binds with high specificity and low nanomolar affinity to the backside of the ERAD ubiquitin-conjugating enzyme (E2) UBE2G2. The structure of the AUP1 G2BR (G2BR^AUP1) in complex with UBE2G2 reveals an interface that includes a network of salt bridges, hydrogen bonds, and hydrophobic interactions essential for AUP1 function in cells. The G2BR^AUP1shares significant structural conservation with the G2BR found in the E3 ubiquitin ligase gp78 and in vitro can similarly allosterically activate ubiquitination in conjunction with ERAD E3s. In cells, AUP1 is uniquely required to maintain normal levels of UBE2G2; this is due to G2BR^AUP1binding to the E2 and preventing its rapid degradation. In addition, the G2BR^AUP1is required for both ER membrane recruitment of UBE2G2 and for its activation at the ER membrane. Thus, by binding to the backside of a critical ERAD E2, G2BR^AUP1plays multiple critical roles in ERAD.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).