OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Abstract

SUMMARY OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the Protein Data Bank (PDB) archive, has been developed as a global collaboration by the Worldwide Protein Data Bank (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

New tools for the analysis and validation of cryo-EM maps and atomic models

“…As a result of our analysis, we advocate for a formal and uniform procedure for validation of atomic models obtained by cryo-EM, as is nowadays available in macromolecular crystallography (Gore et al, 2012), including a cryo-EM-specific validation report, which could be an extension of those currently generated by the wwPDB OneDep system (Young et al, 2017). The lack of such a procedure may result in incorrect interpretations and misuse of deposited atomic models.…”

The data universe of structural biology

“…Concurrent with the work of the VTFs, the wwPDB partners began a project to create a unified system for deposition, curation and validation of structures that have been submitted to the PDB. The recommendations of the VTFs became the basis of the validation suite (Gore et al, 2017) for the new system, called OneDep (Young et al, 2017). The validation report includes most of the indicators recommended by the X-ray VTF including a slider [ Fig.…”

Structural biology data archiving – where we are and what lies ahead

“…The wwPDB partners accept depositions of new structures from their own geographical area (for instance, PDBe is responsible for structures from Europe and Africa). The sites use a common software system, OneDep [16], for the deposition, validation and annotation of the depositions [17]. After approval by the depositors, the processed entries are either released immediately (on a weekly cycle), or withheld until publication or for a maximum period of 1 year.…”

“…It is in the latter area that the spectacular increases in resolution have taken place in the past few years [20]. From 2002 until 2015, the average resolution of single-particle maps deposited to EMDB fluctuated around [15][16][17][18][19][20] A. In the years since then, this number has come down to under 8 A, and in 2017 as many as 315 entries had a resolution better than 4…”