Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Jasmine Young ,Junko Sato,Ardan Patwardhan,Lora Mak,Minyu Chen,Dimitris Dimitropoulos,Eduardo Sanz-García,Irina Persikova,Kayoko Nishiyama,Haruki Nakamura,Ezra Peisach,Sutapa Ghosh,Raul Sala,Genji Kurisu,Yasuyo Ikegawa,Glen Van Ginkel,Sameer Velankar,Aleksandras Gutmanas,Vladimir Guranovic,Chenghua Shao,Sanchayita Sen,Abhik Mukhopadhyay,Gaurav Sahni,Swanand Gore,Lihua Tan,Kumaran Baskaran,Yumiko Kengaku,Luigi Di Costanzo,Huanwang Yang,Li Chen,Thomas J Oldfield ,Jawahar Swaminathan ,Helen M Berman ,Buvaneswari Coimbatore Narayanan ,Brian P Hudson ,David Armstrong ,Marina A Zhuravleva ,Catherine L Lawson ,John L Markley ,Yu-He Liang ,Alice R Clark ,Zhang Feng ,Gerard J Kleywegt ,John M Berrisford ,Guo-Jian Gao ,Ryo Igarashi ,John D Westbrook ,Pieter Hendrickx ,Oliver S Smart ,Monica Sekharan ,S.k Burley

doi:10.1093/database/bay002

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 PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/

Highlights

The Protein Data Bank [1] (PDB, pdb.org) was established in 1971 with just seven X-ray crystal structures and was the first open-access digital biological data resource
The PDB is the single global archive for 3D macromolecular structure data, containing >130 000 structures determined by macromolecular crystallography (MX; using X-ray photons, electrons or neutrons), nuclear magnetic resonance (NMR) spectroscopy and electron cryomicroscopy (3DEM) methods
We describe in detail the processes, practices and tools that wwPDB regional data centers employ during biocuration of PDB structure deposition

Summary

Introduction

The Protein Data Bank [1] (PDB, pdb.org) was established in 1971 with just seven X-ray crystal structures and was the first open-access digital biological data resource. Once the wwPDB biocuration process is complete, Biocurators summarize any outstanding issues in a standardized letter, much of which is generated automatically This summary letter along with the atomic coordinates, experimental data and wwPDB validation report are all made available to the Data Depositor through the OneDep deposition user interface. The Data Depositor receives an email notification to log back into the OneDep system and review the curated data files and the wwPDB validation report At this stage, corrections may be requested to remedy any major issues identified during biocuration, such as polymer chain breaks, stereochemical (chirality) errors in residues or ligands and interatomic clashes. The OneDep system contains functionality to support remediation efforts, making them more efficient

Keeping pace with new developments in structure-determination techniques

Scaling up the day-to-day operations

Findings

Training and retention of workforce