Training, Outreach, and Education

Proteins are polymers of amino acids. The secondary structure elements are beta sheets, alpha helices and loops. These elements are arranged in 3D space creating the environment for the protein or protein domain to fulfill its function.

As more and more 3D shapes became known, researchers noticed patterns in the folding of whole proteins or protein domains.

Visit PDB-101 to download printable alpha helices and beta strand templates for hands-on exploration of many protein folding domains found in the PDB, including the TIM Barrel/Alpha-Beta Barrel, Beta Sandwich/Nanobody, and ABA Sandwich/Rossman Fold.

PDB-101's collection of paper model templates also includes GFP, tRNA, viruses, and more.

Evolution is a natural process where organisms compete in whatever environmental niche they occupy, and the best ones survive and succeed in the "game of life.” Organisms that are less able to compete go extinct. All of this happens without the need for intelligent intervention or design, albeit very slowly most of the time. Scientists believe that all species of living organisms on Earth arose through evolution from simple primordial unicellular organisms.

Looking at the structures of biological molecules, we can explore how evolution has shaped modern proteins and nucleic acids, and search for clues about the molecular nature of the first living things. Scientists are also mimicking the natural processes of evolution in the laboratory, using it to improve the functional properties of proteins and nucleic acids under “artificial” selection pressure.

A new PDB-101 feature explores how evolution is a natural process that produces improved organisms without any need for intelligent intervention.

Since 2014, PDB-101 has focused on different topics to help build a collection molecular stories around a particular theme. Past topics have included cancer and diabetes.

In 2024, PDB-101 will highlight the structural stories of Peak Performance: the structural biology of athletics and well-being.

Athletes require bodies that are the best that is possible, all the way from molecules to muscles. By understanding the structure and function of our molecules, athletes can ensure that they are performing at their peak. This knowledge also informs the ways that we all can live our best lives, at all stages of our lives.

1. PDB structures are used to discuss antibiotics and antivirals, chemotherapy, drug metabolism, drugs of signaling proteins, and lifestyle drugs. How Do Drugs Work? is available as a downloadable flyer and poster. 2. The Insulin and Diabetes poster illustrates how structural biology has revealed the details of insulin signaling and how this knowledge is being used to create new and better treatments for diabetes. 3. Molecule of the Month: Vitamin D. Receptor.  Vitamin D helps regulate the use of calcium throughout the body

The wwPDB Foundation made an award for outstanding student presentations at the 2024 DiscoverBMB Meeting of the American Society for Biochemistry and Molecular Biology (March 23–26, San Antonio, TX).

Solution Structure of the hMDH2-hCS Metabolon
Angela Kayll(1), Harrison Tarbox(2), Andrew Pulido(2), Joseph Provost(2), Christopher E. Berndsen(1)
 (1)Department of Chemistry and Biochemistry, James Madison University
 (2)Department of Chemistry and Biochemistry, University of San Diego

Many thanks to The Biophysical Society organizers and poster prize judges for making this award possible.
The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

The wwPDB Foundation is grateful for our industrial sponsors: Dectris and Discngine. Individual sponsorships are also available.

Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation.

Download the 2023 Annual Report (PDF) for an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Training, Outreach, and Education activities.

This review also highlights RCSB PDB APIs and pairwise alignment tools.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive.

PDB-101 hosts a growing collection of molecular animations that tell some of the structural stories found in the PDB archive. Some highlights from this collection of Videos include:

An Introduction to Neurotransmission and Action Potential.

The billions of neurons in our nervous system are constantly communicating. The signals they send to each other are responsible for our thoughts, sensations, and actions. Learn how ions, ion channels, receptors, and neurotransmitters work together to enable the neuronal signaling process.

Immunology and Cancer

Visit PDB-101 to watch a three-part series exploring the cellular and molecular details of the human immune response to cancer.

Part 1 showcases the process of antigen harvesting by dendritic cells and later the T-cell maturation process. Part 2 focuses on T-cell activation and demonstrates the mechanisms by which the immune system destroys the cancer cells. Part 3 focuses on the immune checkpoints--a mechanism by which the immune system terminates the immune response and later describes the immune checkpoint therapies used in cancer treatment.

Key actions in the video are timestamped for easy access; high resolution images and animated GIFs are also available for download.

Read how RCSB.org provides important tools and resources to search, visualize, and analyze experimentally-determined 3D biostructures alongside computed structure models of proteins predicted using artificial intelligence/machine learning-based tools. PDB-Dev, a prototype system supporting integrative or hybrid methods structural biology, and RCSB PDB training resources available from PDB-101 are also described.

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

Stephen K. Burley, Dennis W. Piehl, Brinda Vallat, Christine Zardecki
(2024) IUCrJ 11: 279-286 doi: 10.1107/S2052252524002604

This article is part of a collection of articles from the IUCr 2023 Congress in Melbourne, Australia, and commemorates the 75th anniversary of the International Union of Crystallography. It describes presentations made by RCSB PDB team members at the meeting in August 2023