Collaborating With Glycoscience Community To Improve Data Representation of Carbohydrates in the Protein Data Bank

Abstract

The Protein Data Bank (PDB) is the single global repository for experimentally‐determined 3D structures of biological macromolecules and their complexes with ligands. The Worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR Principles: Findability, Accessibility, Interoperability, and Reusability. The PDB archive now holds more than 150,000 structures, which are all publicly accessible without restriction.A major focus of the wwPDB is maintaining consistency and accuracy across the archive. As the PDB grows, developments in structure determination methods and technologies can challenge how all structures are represented. The wwPDB addresses these challenges with “remediation” efforts to improve data representation in support of making PDB data FAIR.Understanding the structure and organization of carbohydrates is critical to comprehending their biological roles in health and disease. Approximately 10% of PDB structures contain carbohydrates. However, there is lack of uniform representation for carbohydrates due to complex nature of carbohydrates, which exhibit stereo‐isomers, anomeric configurations, and branched chains. As a result, glycoscientists and other experts are unable to fully utilize the rich structural information available for these structures.Working with the glycoscience community, carbohydrate‐appropriate annotation tools are being developed and implemented within the OneDep system for deposition, validation, and biocuration of PDB structures. These software tools will provide standard nomenclature and consistent oligosaccharide representation that can be easily translated to other representations commonly used by glycobiologists.wwPDB carbohydrate remediation efforts involve: (1) standardizing sugar nomenclature following IUPAC/IUBMB; (2) providing a uniform polymer representation for polysaccharides with appropriate descriptor(s); (3) adopting community software for reliable carbohydrate identification, assignment of standard nomenclature, and detection of intra/inter‐molecular connectivity between monosaccharides and other molecules/proteins; and (4) providing intra‐ and inter‐molecular connectivity at atom level explicitly.Support or Funding InformationThis carbohydrate remediation project is a collaborative wwPDB project carried out principally by the RCSB PDB with funding from NIGMS (U01 CA221216) in collaboration with the Complex Carbohydrate Research Center at the University of Georgia. RCSB PDB is funded by the NSF (DBI‐1832184), the US DOE (DE‐SC0019749), and the NCI, NIAID, and of the NIH under grant R01GM133198.N‐Glycosylation of cardosin A in PDB structure 1b5f (Frazao, C. et al. (1999) J Biol Chem 274: 27694–27701)Figure 1