wwPDB 2021 News

Contents

03/02/2021 More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available
01/14/2021 PDB50: Registration Open for Virtual Event
01/12/2021 wwPDB EM Validation Reports Now Publicly Available
01/06/2021 Time-stamped Copies of wwPDB Archives

03/02/2021

More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available

With this week's update, 1,018 SARS-CoV-2-related structures are now freely available from the Protein Data Bank.

The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7), was released early in the pandemic on February 5, 2020.

Since then, structural biologists have visualized most of the SARS-CoV-2 proteome, including the spike protein binding to its ACE2 receptor and neutralizing antibodies, and the main protease, the papain-like proteinase, and other promising drug discovery targets. All of the structures and related data are available for exploration from wwPDB partner websites: RCSB PDB, PDBe, PDBj, and BMRB.

Rapid public release of SARS-CoV-2 structure data has greatly increased our understanding of Covid-19, allowed direct visualization of emerging variants of the virus, and facilitated structure-guided drug discovery and reuse to combat infection. Open access to PDB structures has already enabled design of effective vaccines against SARS-CoV-2.

The response of the research community to the pandemic has highlighted the importance of open access to scientific data in real time. The wwPDB strives to ensure that 3D biological structure data remain freely accessible for all, while maintaining as comprehensive and accurate an archive as possible.

The impact of these 1018 structures and many more coronavirus protein structures to come stands as a testament to the importance of open access to structural biology research data.

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: <a href="http://pdb101.rcsb.org/sci-art/goodsell-gallery/respiratory-droplet">10.2210/rcsb_pdb/goodsell-gallery-024</a>Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-024

01/14/2021

PDB50: Registration Open for Virtual Event

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Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive.

The inaugural symposium will be held May 4-5, 2021 in an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB Foundation.

This celebration of the 50th anniversary of the founding of the Protein Data Bank as the first open access digital data resource in biology will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics.

Attendees are encouraged to participate in the virtual poster session and exhibition hall. Students and postdoctoral fellows will be eligible for poster awards.

Register and submit abstracts by March 15th, 2021 for reduced rates.

Speakers will include:

  • Edward Arnold - Rutgers, The State University of New Jersey
  • Helen M. Berman - Rutgers, The State University of New Jersey and University of Southern California
  • Thomas L. Blundell - University of Cambridge
  • Alexandre M. J. J. Bonvin - Utrecht University
  • Stephen K. Burley - Rutgers, The State University of New Jersey and University of California San Diego
  • Wah Chiu - Stanford University
  • Johann Deisenhofer - University of Texas Southwestern Medical Center
  • Juli Feigon - University of California Los Angeles
  • Angela M. Gronenborn - University of Pittsburgh
  • Jennifer L. Martin - University of Wollongong
  • Stephen L. Mayo - California Institute of Technology
  • Zihe Rao - ShanghaiTech University and Tsinghua University
  • Hao Wu - Boston Children's Hospital and Harvard Medical School

The online sessions will take place between 11 a.m. – 4:30 p.m. EST each day. The event will be recorded and made available to registered participants after the meeting.

Sponsorship opportunities are available; please contact the wwPDB Foundation for more information.

01/12/2021

wwPDB EM Validation Reports Now Publicly Available

The wwPDB archive has now been updated to include validation reports for every released set of EM model coordinates in the PDB and every released EMDB map entry. Validation reports provide quantitative and visual assessments of structure quality and enable archive-wide comparisons (https://www.wwpdb.org/validation/validation-reports).

wwPDB EM validation reports were first made available to OneDep depositors in 2019 (http://www.wwpdb.org/news/news?year=2019#5db841ceea7d0653b99c8839). The current reports are based on recommendations obtained from EM Validation Task Force (VTF) meetings in 2010 (Structure 20: 205-214, wwpdb.org/task/em) and 2020 (white paper in preparation), as well as EM Validation Challenge events (https://www.ncbi.nlm.nih.gov/pubmed/32002441, https://www.biorxiv.org/content/10.1101/2020.06.12.147033v1). Examples of recent improvements include images for deposited masks, improved map-model overlay images, visualization of a (approximate) raw map from two half-maps, and rotationally averaged power spectrum plots. The underlying methodology is continually improved, based on community requirements, requests and feedback.

The PDB Core Archive holds validation reports that assess each PDB model along with its associated experimental map/tomogram from EMDB. EM map+model reports can be downloaded at the following wwPDB mirrors:

The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. EM map-only reports can be downloaded at the following URLs:

Additional information about validation reports is available for EM map+model, EM map only, and EM tomograms.

If you have any questions or queries about wwPDB validation, please contact us at validation@mail.wwpdb.org.

Example of map-model overlay image: EMD-30388/7CWU, SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktailExample of map-model overlay image: EMD-30388/7CWU, SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktail

01/06/2021

Time-stamped Copies of wwPDB Archives

A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 5th, 2021 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20210105 includes the structure and experimental data for the 173,005 PDB entries available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core archive is 822 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 4, 2021 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20210101/ and ftp://snapshots.pdbj.org/20210101/. The snapshot of EMDB Core archive contains map files and their metadata within XML files for both released and obsoleted entries (13731 and 142, respectively) and is 2.9 TB in size.