Training, Outreach, and Education

In July 2023, the Worldwide Protein Data Bank celebrated its 20th anniversary by welcoming Protein Data Bank China (PDBc) to the organization as an Associate Member (Acta Cryst. (2023). D79, 792-795). 

The celebrations continued with an estimated 1700 members of the structural science community at the 2023 Congress and General Assembly of the International Union of Crystallography (IUCr) in Melbourne, Australia.  

Attendees visited the wwPDB exhibit stand to celebrate how many of the 200,000+ structures in the archive they have deposited. At the exhibit booth, depositors learned how they can access their depositions using ORCiDs and how to prepare depositions with pdb_extract.  Also in the exhibit hall, the Bragg Your Pattern team hosted ~800 students for hands-on activities and learning, including PDB-101’s virus building activity (see the April 2023 Education Corner for more on Bragg Your Pattern).

Presentations included RCSB PDB Director Stephen Burley’s keynote that explored SARS-CoV-2 using perspectives from structural biology, drug discovery, funding, and beyond.  PDBj Head gave an overview of Protein Data Bank Japan: the Asian hub of 3D macromolecular structural data.

Other presentations from RCSB PDB team members included PDB-Dev: A prototype system for archiving integrative structures (Brinda Vallat); Exploring experimentally-determined structures and computed structure models from artificial intelligence/machine learning at RCSB PDB (Dennis Piehl), and RCSB PDB: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education (Christine Zardecki).

Collage of IUCr activities, clockwise from upper left: Bragg Your Pattern virus building; depositors showing their deposition numbers; the wwPDB exhibition stand; Atsushi Nakagawa and Genji Kurisu (PDBj).

At this year's meeting of ACA: The Structural Science Society, the RCSB PDB Poster Prize award went to Alexander Paredes.

Biophysical characterization of the Pseudomonas aeruginosa BqsR/BqsS two-component system

Alexander Paredes (University of Maryland Baltimore County, UMBC), Janae Baptiste-Brown (Spelman College), Chioma Iheacho (UMBC), Aaron T Smith (UMBC)

Many thanks to the Poster Chairs Sara Andres (McMaster University) and Leighanne Gallington (Argonne National Laboratory), the judges and the ACA.

At this year's Intelligent Systems for Molecular Biology (ISMB) conference, the RCSB PDB Poster Prize award went to Nele Quast.

A Structure-Focused Analysis of Antigens Presented by the Class 1 Major Histocompatibility Complex

Nele Quast, Matthew Raybould, Charlotte Deane (University of Oxford)

Many thanks to judges Yuhe Liang and Chenghua Shao (RCSB PDB) and to Steven Leard (ISMB) for his continued support.

Some of bacterial ribosome-inactivating toxins evolved to mimic the mechanism employed for loading onto the ribosome by translation factors. The illustration depicts how Shiga toxin 2a (Stx2a) holotoxin (green, PDB ID: 7U6V, EMD-26381) outcompetes the EF-Tu elongation factor (red, PDB ID: 1TTT) complexed with Phe-tRNAPhe (orange) for binding to the ribosomal P-stalk (red) at the large subunit of the 80S ribosome (purple, EMD-26380). Kulczyk et al. determined a cryo-EM structure of Stx2a bound to the native ribosomal P-stalk. The illustration was created by Maria Voigt (RCSB PDB) with materials provided by Arek Kulczyk (Rutgers University, Institute for Quantitative Biomedicine).

This image appeared on the March 2023 cover of the Journal of Biological Chemistry.

Visit PDB-101 to download a high resolution version of the image

A new PDB-101 feature explores how cells capture and utilize many forms of energy to power their molecular processes

Cells expend much of their effort manipulating the environment around them to their advantage. Doing so takes a lot of energy, for example, to power finding food sources, eating and digesting food molecules, and using these molecules to build new cells. For this reason, cells are masters at harnessing diverse sources of energy and putting them to use. Structural biologists are exploring biomolecules that capture and convert energy in cellular processes. New, advanced techniques are being used to reveal the structure and function of these molecules: continued improvement in the resolution of cryoelectron microscopy is revealing complex and larger protein assemblies involved in bioenergy, and split-second serial crystallography with X-ray free electron lasers is giving a close-up look at rapid energetic transitions.

PDB structures provide insight into the mechanisms and technology of bioenergy.

Visit PDB-101 for more.

RCSB PDB is highlighted in the Spring-Summer issue of EdgeDiscovery, a publication that highlights research and research computing initiatives in New Jersey and beyond.