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. 2021 Jan 8;49(D1):D437-D451.
doi: 10.1093/nar/gkaa1038.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley  1   2   3   4   5 , Charmi Bhikadiya  1   2 , Chunxiao Bi  4 , Sebastian Bittrich  4 , Li Chen  1   2 , Gregg V Crichlow  1   2 , Cole H Christie  4 , Kenneth Dalenberg  1   2 , Luigi Di Costanzo  1   2 , Jose M Duarte  4 , Shuchismita Dutta  1   2   3 , Zukang Feng  1   2 , Sai Ganesan  6 , David S Goodsell  1   2   7 , Sutapa Ghosh  1   2 , Rachel Kramer Green  1   2 , Vladimir Guranović  1   2 , Dmytro Guzenko  4 , Brian P Hudson  1   2 , Catherine L Lawson  1   2 , Yuhe Liang  1   2 , Robert Lowe  1   2 , Harry Namkoong  1   2 , Ezra Peisach  1   2 , Irina Persikova  1   2 , Chris Randle  4 , Alexander Rose  4 , Yana Rose  4 , Andrej Sali  6 , Joan Segura  4 , Monica Sekharan  1   2 , Chenghua Shao  1   2 , Yi-Ping Tao  1   2 , Maria Voigt  1   2 , John D Westbrook  1   2   3 , Jasmine Y Young  1   2 , Christine Zardecki  1   2 , Marina Zhuravleva  1   2
Affiliations

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1.
Figure 1.
Using Basic Search to find structures. (A) In addition to single PDB ID searches, the interface supports multiple IDs when separated by a space or comma plus space. Search results are returned in a summary view with options for display and report generation. (B) Entering text (e.g. SARS-CoV-2) launches a drop-down menu of suggested searches organized by category. (C) Clicking on Source Organism Taxonomy Name>SARS-CoV-2 yields all currently available SARS-CoV-2 protein structures in the PDB. Highlighted are options to refine the results set by attribute and to sort the results by Score (measure between 0 and 1 intended to reflect the degree of relevance with which the listed structure matches the input search term), Release Date, PDB ID and Resolution.
Figure 2.
Figure 2.
Advanced Search Query Builder used for a search where Source Organism Taxonomy Name = Coronaviridae AND structures that are ≥50% identical to the sequence of PDB ID 1Q2W [SARS-CoV Nsp5 (27)] AND structures similar in structure (relaxed) to PDB ID 6LU7 [SARS-CoV-2 Nsp5 (15)] AND structures matching the SMILES string for a small-molecule inhibitor designated 7J (PDB CCD QYS). This search yielded three structures matching all criteria, including co-crystal structures with the desired bound inhibitor (7J/QYS) for SARS-CoV-2 Nsp5 [6XMK (40)], SARS-CoV Nsp5 [6W2A (40)] and MERS-CoV Nsp5 [6VH3 (40)]. Advanced Search results can be displayed as Structures (or Entities), individual polymer Entities, Assemblies or non-polymer Entities.
Figure 3.
Figure 3.
Structure Summary Page features for the SARS-CoV-2 Spike protein [6VXX (21)], which includes (A) top-line summary plus dedicated content boxes for Literature, tools for exploring (B) Macromolecules, (C) Oligosaccharides and Ligands, and (D) Experimental Data & Validation and Entry History & Funding Information, plus links to other features.
Figure 4.
Figure 4.
The Structure Summary Sequence tab for the SARS-CoV-2 Spike protein [6VXX (21)] provides access to the entire sequence of each Entity Instance comprising the Entry in the Protein Feature View tool.
Figure 5.
Figure 5.
Protein Feature View for a UniProtKB sequence provides a graphical summary of the alignments between the selected reference sequence and all its related PDB Entities (e.g. P0DTC2). (A) Default display shows the alignment between the selected UniProtKB sequence and all its related PDB Entities (e.g. ALL) versus (B) zoomed in display of optional PDB Instance one at a time for 6VSB_1>A showing the UNIPROT ALIGN and the PDB INSTANCE ALIGN amino acid sequences.
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References

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