[3dem] Celebrating 20 Years of the wwPDB
Justin Flatt
justin at rcsb.rutgers.edu
Wed Jul 12 13:22:53 PDT 2023
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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[1] https://urldefense.com/v3/__https://www.wwpdb.org/__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoZjbIi_3$
[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$
[4] https://urldefense.com/v3/__https://pdbj.org/__;!!Mih3wA!AB5HhIUeSU-pZa3eVRVM_kQm3YiYMaDtWY9IWrPUdv6AwXnSDdU-YVsvGjWO3uWaBO8w2ZYuEy9O1RuFoYSWx_ss$
[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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