Celebrating 20 Years of the wwPDB

07/09 

The Worldwide Protein Data Bank celebrates its 20th anniversary in 2023

In July 2003, the Worldwide Protein Data Bank was launched as a partnership between RCSB Protein Data Bank (RCSB PDB, USA), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj) in the management of the essential Protein Data Bank Core Archive of atomic-level, three-dimensional (3D) structures of biological macromolecule experimentally determined by macromolecular crystallography (MX), nuclear magnetic resonance (NMR) spectroscopy, or three-dimensional cryo-electron microscopy (3DEM; 1, 2).

Since then, the wwPDB collaboration has expanded to include additional Core Archives as partners: BioMagResBank (BMRB, USA) Core Archive of spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites; and Electron Microscopy Data Bank (EMDB, UK) Core Archives of 3D volumes and associated information of macromolecular complexes and subcellular structures from 3DEM and electron cryo tomography. wwPDB partners adhere to the FAIR principles of Findability, Accessibility, Interoperability, and Reusability (2), and ensure that all archival data can be accessed at no charge and with no limitations on usage under the most permissive Creative Commons CC0 1.0 Universal License.

As the wwPDB celebrates its twentieth year of operations, wwPDB is pleased to welcome Protein Data Bank China (PDBc) to the organization as an Associate Member. PDBc is based in the National Facility for Protein Science in Shanghai which is associated with Shanghai Advanced Research Institute of Chinese Academy of Sciences, and the SIAIS and iHuman Institutes of ShanghaiTech University. An announcement describing the process of PDBc joining the wwPDB has been submitted to Acta Cryst D (PDF, 3). PDBc has received training and support from the wwPDB partners, and it is expected that PDBc will process most, possibly all, depositions made by structural biologists working in the People’s Republic of China to all three wwPDB Core Archives.

Since its inception, the PDB has been an international archive and the establishment of the wwPDB ensured that valuable data contained in these Core Archives will continue to be stored, managed and kept freely available for the benefit of scientists worldwide.

• (1) Helen M. Berman, Kim Henrick, Haruki Nakamura. (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980. doi: 10.1038/nsb1203-980
• (2) wwPDB consortium (2019) Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Research 47:D520–D528 doi: 10.1093/nar/gky949
• (3) Wenqing Xu, Sameer Velankar, Ardan Patwardhan, Jeffrey C. Hoch, Stephen K. Burley, Genji Kurisu (2023) Announcing launch of Protein Data Bank China (PDBc) as an Associate Member of the Worldwide Protein Data Bank (wwPDB) Partnership (2023) Acta Cryst. D79 792-795 doi: