Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

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Authors

APPASAMY Sri Devan BERRISFORD John GÁBOROVÁ Romana NAIR Sreenath ANYANGO Stephen GRUDININ Sergei DESHPANDE Mandar ARMSTRONG David PIDRUCHNA Ivanna ELLAWAY Joseph I. J. LEINES Grisell Díaz GUPTA Deepti HARRUS Deborah VARADI Mihaly VELANKAR Sameer

Year of publication 2023
Type Article in Periodical
Magazine / Source Scientific Data
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://doi.org/10.1038/s41597-023-02778-9
Doi http://dx.doi.org/10.1038/s41597-023-02778-9
Keywords CRYSTAL-STRUCTURE; 20S PROTEASOME; MECHANISM; PDB; ASSEMBLIES; RECEPTOR; REVEALS; RESOURCE; YEAST; STATE
Description Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB’s FAIR attributes, fostering more effective basic and translational research and scientific education.
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