Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

TY - JOUR

T1 - Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

AU - Shao, Chenghua

AU - Feng, Zukang

AU - Westbrook, John D.

AU - Peisach, Ezra

AU - Berrisford, John

AU - Ikegawa, Yasuyo

AU - Kurisu, Genji

AU - Velankar, Sameer

AU - Burley, Stephen K.

AU - Young, Jasmine Y.

N1 - Publisher Copyright: © 2021 The Author(s) 2021. Published by Oxford University Press. All rights reserved.

PY - 2021/9/1

Y1 - 2021/9/1

N2 - 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.

AB - 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.

KW - Protein Data Bank

KW - carbohydrate structure

KW - glycan

KW - glycosylation

KW - oligosaccharide

UR - http://www.scopus.com/inward/record.url?scp=85117060996&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85117060996&partnerID=8YFLogxK

U2 - https://doi.org/10.1093/glycob/cwab039

DO - https://doi.org/10.1093/glycob/cwab039

M3 - Article

C2 - 33978738

SN - 0959-6658

VL - 31

SP - 1204

EP - 1218

JO - Glycobiology

JF - Glycobiology

IS - 9

ER -