Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

Author:

Shao Chenghua1,Feng Zukang1,Westbrook John D12,Peisach Ezra1,Berrisford John3,Ikegawa Yasuyo4,Kurisu Genji4,Velankar Sameer3,Burley Stephen K1256,Young Jasmine Y1

Affiliation:

1. Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

2. Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA

3. Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

4. Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan

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

6. Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

Abstract

Abstract Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability–Accessibility–Interoperability–Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.

Funder

National Institutes of Health Common Fund Glycoscience Program

National Science Foundation

US Department of Energy

National Cancer Institute, National Institute of Allergy and Infectious Diseases

National Institutes of Health

National Bioscience Database Center

Publisher

Oxford University Press (OUP)

Subject

Biochemistry

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