Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

Area of Science:

• Structural Biology
• Bioinformatics
• Data Archiving

Background:

• The Protein Data Bank (PDB) was established in 1971 as the first open-access digital resource for biological sciences.
• It currently archives approximately 130,000 experimentally determined 3D structures of biological macromolecules.
• The PDB is managed globally by the Worldwide Protein Data Bank (wwPDB) organization, comprising four partners: RCSB PDB, PDBj, PDBe, and BMRB.

Purpose of the Study:

• To describe the management and operational structure of the Protein Data Bank (PDB) by the Worldwide Protein Data Bank (wwPDB).
• To highlight the unified global software system ensuring data standards, deposition, biocuration, and validation.
• To outline the current data archiving capabilities and future expansion into integrative/hybrid methods.

Main Methods:

• Unified global software system for data deposition, biocuration, and validation.
• Archiving of experimental data, metadata, and 3D atomic models from crystallography, NMR, and 3DEM.
• Collaboration with experts to establish a federation for integrative/hybrid methods data.

Main Results:

• The PDB archives ~130,000 entries, with ~11,000 new entries processed annually.
• A unified system ensures consistent data standards across wwPDB partners.
• Complementary websites offer diverse views and links to related data resources.

Conclusions:

• The wwPDB provides a robust and unified system for archiving and validating 3D structural data.
• The PDB is expanding to include data from integrative/hybrid experimental methods.
• This ensures sustainable archiving and accessibility of biological macromolecular structure data.