PDB-101: Educational resources supporting molecular explorations through biology and medicine

Abstract

The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic-level three-dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB-101 was launched to support teachers, students, and the general public in PDB archive exploration (pdb101.rcsb.org). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB-101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB-101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year-on-year. In addition, PDB-101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB-101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Keywords: PDB; Protein Data Bank; education; protein structure and function; structural biology; training.

FIGURE 1

Molecular Machinery posters produced in 2002 (left) and 2014 (right). The enormous range of molecular shapes and sizes in the Protein Data Bank (PDB) is illustrated by these molecular machines. The first poster was one of the earliest outreach projects from the Research Collaboratory for Structural Bioinformatics PDB, in addition to the Molecule of the Month (MOTM) series. This printed poster was distributed to thousands of PDB users, teachers, and students over the years. The graphic was updated in 2014 to celebrate the milestone of 100,000 released PDB structures. The updated version reflects the increase in structural complexity in the archive and demonstrates PDB‐101's emphasis on storytelling. Structures are depicted relative to the cellular membrane and organized in various categories related to function. A scale bar provides a sense of molecular size in nanometers. The 2014 edition is available as a poster, flyer, and interactive animation; most of the structures shown are highlighted in MOTM articles. All related materials are available from https://pdb101.rcsb.org/learn/flyers‐posters‐and‐other‐resources/flyer/molecular‐machinery‐a‐tour‐of‐the‐protein‐data‐bank

FIGURE 2

PDB‐101 categories. Users can browse these categories to find corresponding content and activities at https://pdb101.rcsb.org/browse

FIGURE 3

Selected Molecule of the Month (MOTM) topics from 2021. These articles were written and illustrated by students in collaboration with PDB‐101 as part of a week‐long boot camp on “Science Communication in Biology and Medicine” for undergraduate and graduate students hosted by the Rutgers Institute for Quantitative Biomedicine in January 2021. MOTM articles organized by year can be accessed at https://pdb101.rcsb.org/motm/motm‐by‐date

FIGURE 4

Still image from the video Opioids and Pain Signaling of a neuronal synapse with vesicles and relevant proteins highlighted (https://pdb101.rcsb.org/learn/videos/opioids‐and‐pain‐signaling)

FIGURE 5

SciArt Gallery Examples. Left: Myoglobin Fold, 1987, by Irving Geis. Available from https://pdb101.rcsb.org/sci‐art/geis‐archive/gallery/rcsb‐0001‐myoglobin‐fold; used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved. Right: Myoglobin in a Whale Muscle Cell, 2021, illustration by David S. Goodsell, Research Collaboratory for Structural Bioinformatics Protein Data Bank (PDB). doi: 10.2210/rcsb_pdb/goodsell‐gallery‐032. SciArt pages at PDB‐101 were accessed more than 196,000 times in 2020