Protein Data Bank

The RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank) is the US-based data center that curates and distributes data for the global Protein Data Bank (PDB) archive.

It is the world’s leading repository for information about the three-dimensional shapes of biological macromolecules, such as proteins and nucleic acids. Its mission is to enable breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of these structures.

Core Data & Holdings

The RCSB PDB is a massive, constantly growing archive that provides access to two primary classes of structural data:

1. Experimentally-determined 3D Structures: These are structures determined using biophysical methods like X-ray crystallography, NMR spectroscopy, and Cryo-electron microscopy (Cryo-EM). These entries form the core PDB archive (over 245,000 structures).
2. Computed Structure Models (CSM): The site has integrated over a million computed models from resources like AlphaFold DB and ModelArchive, which are typically generated using Artificial Intelligence/Machine Learning methods. This significantly expands the coverage of the known proteome.

The mission of RCSB PDB is to archive, validate, curate, and disseminate high-quality biomolecular structures obtained through:

• X-ray crystallography
• Cryo-electron microscopy (cryo-EM)
• Nuclear magnetic resonance (NMR) spectroscopy
• Hybrid and integrative methods

Its commitment to openness ensures that structural data produced in publicly funded research is accessible to scientists worldwide, accelerating discovery and reproducibility.

RCSB PDB underpins research in:

• Molecular biology
• Structural bioinformatics
• Computational chemistry
• Drug design
• Biophysics
• Systems biology
• Evolutionary studies

Key Services and Functionality

The RCSB PDB website (rcsb.org) is a comprehensive resource divided into several major functional areas:

1. Search and Discovery

The platform offers powerful methods for locating structures:

• Advanced Search: Allows for complex boolean queries using a wide range of structure attributes.
• Sequence Similarity Search: Find proteins or nucleic acids that have similar sequences to your input (uses the mmseqs2 method).
• Structure Similarity Search: Search for structures based on their overall 3D shape, regardless of sequence.
• Chemical Similarity Search: Identify ligands or small molecules bound to macromolecules by searching with a SMILES string, InChI, or chemical formula.

2. Visualization and Analysis

Users can deeply investigate individual structures and compare them to others:

• Mol* (MolStar): The primary, modern 3D visualization tool accessible directly from every structure summary page. It allows users to explore the atomic coordinates, ligand binding sites, and biological assemblies. * Sequence Annotations Viewer: Provides graphical summaries of protein features and their relationship with external databases like UniProtKB.
• Pairwise Structure Alignment: Calculate alignments between two structures using various computational methods.
• Structure Quality: Tools to compare important global quality indicators of a given structure against the entire PDB archive.

3. Data Deposition and Validation

RCSB PDB is part of the worldwide wwPDB consortium and provides the necessary tools for scientists to formally submit their data:

• wwPDB OneDep System: The central system for depositing 3D macromolecular structure data.
• Validation Server: Enables researchers to check the quality of their X-ray, NMR, or EM structures before deposition, ensuring data meets global standards.
• Data Preparation Tools: Includes utilities like Ligand Expo (for finding chemical component IDs) and MAXIT (for file format translation).

4. Learning and Education (PDB-101)

The PDB-101 section is dedicated to educational outreach:

• Molecule of the Month: A highly popular resource that provides engaging, guided accounts of selected molecules from the PDB, explaining their biological function and relevance.
• Educational Resources and Curricula: Authentic, hands-on teaching materials and activities for students and teachers.
• SciArt Galleries: Features molecular art from pioneers like Irving Geis and David Goodsell, promoting the visual aesthetics of structural biology.

Context and Governance

The RCSB PDB is a collaboration funded by the U.S. National Science Foundation (NSF), the US Department of Energy (DOE), and the National Institutes of Health (NIH). It is hosted by a consortium that includes Rutgers University, the University of California San Diego, and the University of California San Francisco, and operates as a core partner of the wwPDB (Worldwide Protein Data Bank) organization.