Data Deposition/Biocuration Services and Archive Management

In 2021, 14,571 experimentally-determined structures were deposited to the archive.  Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

Of all structures deposited this year, 86.9% were deposited with a release status of hold until publication; 7.3% were released as soon as annotation of the entry was complete; and 5.8% were held until a particular date. 68.3% of these entries were determined by X-ray crystallographic methods; 2.5% were determined by NMR methods; and 28.9% by 3DEM.

4,483 EMDB maps were released in the archive.

12,602 new PDB structures were released in 2021. They account for 6.8% of the year-end total holdings of 185,610 available entries.

925 SARS-CoV-2 structures were released.

Starting February 25th, 2022, deposition of half-maps for single-particle, single-particle-based helical and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) will be mandatory. This change is in response to long-standing community requests as well as a recommendation from the 2020 wwPDB single-particle cryo-EM data-management workshop.

Mandatory half-maps must be unfiltered, unmasked, unsharpened, and positioned in the same coordinate-space and orientation as the primary map such that they superimpose. The availability of half-maps will contribute to improved validation of EM structures as reflected in the wwPDB validation reports. For additional details, visit wwPDB.org.

Carbohydrate molecules present in more than 14,000 PDB structures were reviewed and remediated to conform to a new standardized format to facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank
Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach, John Berrisford, Yasuyo Ikegawa, Genji Kurisu, Sameer Velankar, Stephen K Burley, Jasmine Y Young
(2021) Glycobiology 31: 1204–1218, doi:10.1093/glycob/cwab039

Additional documentation about the carbohydrate remediation project is available.

RCSB PDB Biocurators Dr. Sutapa Ghosh and Dr. Monica Sekharan

RCSB PDB Biocurator Dr. Brian P. Hudson talking about the SARS-CoV-2 main protease in February 2020.

Congratulations to biocurators Dr. Sutapa Ghosh, Dr. Monica Sekharan, and Dr. Brian P. Hudson on processing over 10,000 PDB depositions. PDBj's Yumiko Kengaku was the first biocurator to reach this milestone in April 2021.

Drs. Ghosh and Sekharan reached this milestone in the Fall. Dr. Ghosh received her PhD in structural biology from the University of Calcutta and joined PDB after working in industry in structure-based drug design. Dr. Sekharan received her PhD in Biological Chemistry from the University of Washington with expertise in NMR spectroscopy. During their 15 year career at the PDB, many depositors trusted their professional skills in accurate and comprehensive data analysis and representation. 

Dr. Hudson reached this milestone in December.  He received his PhD in Chemistry from the California Institute of Technology and has an expertise in X-ray crystallography and cryo-electron microscopy. He has joined PDB in 2010 and has established himself as a highly qualified professional with deep understanding of scientific data and various experimental techniques and dedication to exceptional quality data curation. He was one of the EM data curation pioneers who curated over 1000 of EM map entries before the OneDep system was established. 

Their deep scientific knowledge, profound data curation expertise and commitment to excellence contributed to the high quality data archive for the benefit of the scientific community. We congratulate these biocurators on this exciting accomplishment and look forward to their future successes.