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

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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.’

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Most cited references 44

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The RCSB protein data bank: integrative view of protein, gene and 3D structural information

Peter W Rose, Andreas Prlić, Ali Altunkaya … (2016)

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.

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Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism

Elizabeth Brunk, Swagatika Sahoo, Daniel C. Zielinski … (2018)

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.

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Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Stephen Burley, Helen Berman, Gerard Kleywegt … (2017)

The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

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Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date (Print): 08 January 2019

Publication date (Electronic): 24 October 2018

Publication date PMC-release: 24 October 2018

Volume: 47

Issue: Database issue , Database issue

Pages: D464-D474

Affiliations

[1 ]Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

[2 ]Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA

[3 ]Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA

[4 ]Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

[5 ]The Scripps Research Institute, La Jolla, CA 92037, USA

Author notes

To whom correspondence should be addressed. Tel: +1 848 445 4924; Fax: +1 848 445 4320; Email: christine.zardecki@ 123456rcsb.org

Present address: Tara Kalro, ResMed, San Diego, CA 92123, USA.

Present address: Andreas Prlić, Structural Bioinformatics Laboratory, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

Present address: Peter Rose, Structural Bioinformatics Laboratory, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

Present address: Raul Sala, Office of Informational Technology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Present address: Jesse Woo, Movemedical, San Diego, CA 92127, USA.

Present address: Huanwang Yang, Comcast, Philadelphia, PA 19103, USA.

Author information

Peter Rose http://orcid.org/0000-0001-9981-9750

Jasmine Young http://orcid.org/0000-0001-8896-6878

Christine Zardecki http://orcid.org/0000-0002-4149-1745

Article

Publisher ID: gky1004

DOI: 10.1093/nar/gky1004

PMC ID: 6324064

PubMed ID: 30357411

SO-VID: d093e882-3ab9-4735-990f-ee31bd2fa00f

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date accepted : 11 October 2018

Date revision received : 27 September 2018

Date received : 14 September 2018

Page count

Pages: 11

Funding

Funded by: National Science Foundation 10.13039/100000001

Award ID: NSF-DBI 1338415

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