RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'

Figure 1.

PDB data life-cycle and RCSB PDB services. RCSB PDB hosts four integrated, interdependent cyberinfrastructure services, supported by a Customer Service Help Desk and IT Support.

Figure 2.

RCSB PDB Services Status page. Public accessibility of all critical project services is monitored and displayed on a dedicated webpage (status.rcsb.org). Percentages shown reflect the availability level of the resource over the previous 24-h period. Service interruptions trigger automatic redirection of User traffic between Rutgers and UCSD, and staff notifications to ensure prompt evaluation resolution. From this page, users can subscribe to an electronic list for related notifications (Status Updates).

Figure 3.

Text search results and options for exploration. Search terms ‘insulin receptor’ enclosed in double quotation marks are indicated on upper left of page. For each entry in the search results, the appearance of the search term in categories relating to author, citation, entity name, entity description, keyword or title is highlighted (under ‘Matched fields,’ highlighted in lower right box). Search results can be sorted by match score, release date, PDB ID, residue count or resolution (highlighted in upper right box). Custom and default reports can be generated and downloaded. Users can also access corresponding data files and Structure Summary pages.

Figure 4.

Features of the NGL 3D Viewer. (A) NGL view of the structure of a hexameric, volume-regulated anion channel of the LRRC8 family (PDB ID: 6g9l (54)), viewed down the ion conducting pore from the cell surface. Polypeptide chain ribbons are colored from N-terminus (blue) to C-terminus (red). Polypeptide chain ribbons are colored from N-terminus (blue) to C-terminus (red). (B) NGL view of the interaction of B-Raf Kinase bound to the US FDA approved anti-neoplastic drug Vemurafenib (PDB ID: 3og7 (55)). Ball-and-stick figure atom color coding (C-gray for drug or white for protein; O-red; N-blue; S-yellow; F-green). Hydrogen bonds are denoted with blue dashed lines, hydrophobic interactions with gray-dashed lines and cation–π interactions with pink-dashed lines.

Figure 5.

EPPIC and 3D NGL ribbon diagram views of CcmP, a tandem bacterial microcompartment domain protein from the beta-carboxysome (PDB ID: 4ht5 (56)). (A) EPPIC assembly graph corresponding to the D3 symmetric assembly with the NGL view of the same assembly. Nodes denote proteins and edges denote interfaces between proteins, colored to represent distinct modes of protein–protein interaction. (B) Same structure in NGL viewer. Polypeptide chain ribbons are colored from N-terminus (blue) to C-terminus (red).

Figure 6.

PDB Metrics: growth of new 3DEM structures in the PDB. All statistical charts are updated dynamically each week. Data can be downloaded for external use. This 3DEM growth chart can be accessed at www.rcsb.org/stats/growth/em.