[3dem] Celebrating 20 Years of the wwPDB

[Justin Flatt]

In July 2003, the Worldwide Protein Data Bank [1] was launched as a 
partnership between RCSB Protein Data Bank (RCSB PDB [2], USA), Protein 
Data Bank in Europe (PDBe [3]), Protein Data Bank Japan (PDBj [4]) 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 [5], USA) Core Archive of 
spectral and quantitative data derived from NMR spectroscopic 
investigations of biological macromolecules and metabolites; and 
Electron Microscopy Data Bank (EMDB [6], 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 [7].

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 [8], 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 [9]
  	* (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 [10]
  	* (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 Acta Cryst. D, submitted (PDF [8])



Links:
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[2] https://urldefense.com/v3/__https://rcsb.org__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoYlpv-iO$ 
[3] https://urldefense.com/v3/__https://pdbe.org/__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoezh1P3Z$ 
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[5] https://urldefense.com/v3/__https://bmrb.io/__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoULi6Tc3$ 
[6] https://urldefense.com/v3/__http://emdb-empiar.org/__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoVqeEwPs$ 
[7] https://urldefense.com/v3/__https://www.wwpdb.org/about/usage-policies__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoVlphoam$ 
[8] https://urldefense.com/v3/__https://cdn.rcsb.org/wwpdb/docs/AnnualReport2023.pdf__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoSF_M29h$ 
[9] https://urldefense.com/v3/__https://doi.org/10.1038/nsb1203-980__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFofSoajTh$ 
[10] https://urldefense.com/v3/__https://doi.org/10.1093/nar/gky949__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoYgGIKGn$ 
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