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, 45 (D1), D271-D281

The RCSB Protein Data Bank: Integrative View of Protein, Gene and 3D Structural Information

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The RCSB Protein Data Bank: Integrative View of Protein, Gene and 3D Structural Information

Peter W Rose et al. Nucleic Acids Res.

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

Figures

Figure 1.
Figure 1.
(A) NGL viewer and user interface showing a low-resolution surface of the faustovirus major capsid protein (PDB ID 5J7V) generated from a C-alpha representation. This PDB entry consists of 2760 instances of an asymmetric unit, each containing 14 478 atoms. For fast rendering, the surface of the asymmetric unit is created once, and rotation/translation operations are used to create additional copies of the surface. (B) Unit cell representation (PDB ID 3PQR) created by applying crystallographic symmetry operations from the asymmetric unit. (C) Supercell representation (PDB ID 3PQR) created by translating the unit cell along all three dimensions.
Figure 2.
Figure 2.
(A) Mapping tool from human genomic coordinates to UniProt Isoforms and corresponding locations in a PDB structure. The selected position corresponds to the site of a genetic variation in the hemoglobin beta chain that is known to cause sickle-cell disease. (B) The corresponding position on the protein can be visualized in 3D (PDB ID 1CH4). A similar 3D view is available from the Protein Feature View.
Figure 3.
Figure 3.
The new Pathway View provides graphical representations of metabolic pathways using Escher. Shown here is the Tricarboxylic acid (TCA) or Krebs cycle for human. Color-coding indicates parts of the pathway for which 3D structures are available in the PDB (blue: PDB structures available; yellow: structure can be inferred via homology modeling).
Figure 4.
Figure 4.
The left-hand menu on the homepage provides easy navigation to high-level tasks. In this example Search is selected. The middle panel lists available search options, and in this example, Drill Down by Categories is selected. The associated right panel exposes further drill-down options to select a specific subset of PDB entries.
Figure 5.
Figure 5.
Top section of the Search Results page after a MeSH term search for Diabetes Mellitus. Only a single hit is shown here for brevity. The search results can be refined by clicking on any of the terms in the left-hand panel, e.g. Homo sapiens to limit the result set to structures with protein chains derived from human.
Figure 6.
Figure 6.
Upper portion of the Structure Summary Page for PDB ID 2RH1. Tabs are used to navigate to details including annotations, sequence level information, sequence and structure similarity, experimental details and literature associated with an entry. Blue query by example links launch queries for the selected term. The wwPDB Validation Report slider provides a high level view of various geometric and model fit metrics.
Figure 7.
Figure 7.
Macromolecules section of the Structure Summary Page for PDB ID 5LAP. Top portions summarize detail regarding the polymer chain. A link is provided to the UniProt sequence, and two links allow the user to find similar protein chains by either sequence or structure similarity. The bottom portion shows a simplified version of the Protein Feature View, which includes a PDB Validation track.
Figure 8.
Figure 8.
(A) Small molecule section of the Structure Summary page (PDB ID 1CBS) with 2D chemical diagram, 2D interaction diagram (PoseView) and links to 3D viewers, including an electron density view around the ligand. (B) SigmaA-weighted 2m|Fo|-D|Fc| electron density map for a retinoic acid ligand (REA in PDB ID 1CBS) contoured at 1 sigma level, showing excellent correspondence with the atomic model. (C) SigmaA-weighted 2m|Fo|-D|Fc| electron density map for a thymidine-5′-phosphate ligand (TMP in PDB ID 3HW4) contoured at 1 sigma level, showing poor correspondence with the atomic model.

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