Protein Data Bank: the single global archive for 3D macromolecular structure data

Abstract

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

Figure 1.

(A) Growth the PDB Core Archive. Total height of each bar indicates aggregate released structures, coloured by experimental technique (MX—green, 3DEM—yellow, NMR—blue). (B) Number of PDB structures released annually. All PDB Core Archive structures are indicated with light green shading, and MX structures are shown with a solid green line, plotted with respect to the green primary axis (left). NMR structures (blue solid line) and 3DEM structures (blue dashed line) are plotted with respect to the blue secondary axis (right).

Figure 2.

World map indicating the locations of wwPDB partner sites and color-coded to indicate the regions from which each accepts PDB depositions.

Figure 3.

Quarterly wwPDB structure data file download metrics from 2008–2017 (FTP and rsync downloads-solid line; wwPDB partner website downloads-dotted line).

Figure 4.

Boxplot representation of the number of residues per PDB structure per year. Red lines represent the median value, boxes represent the 25 and 75 percentile values, and whiskers represent the 5th and 95th percentile values.