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. 2022 Dec;31(12):e4482.
doi: 10.1002/pro.4482.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Stephen K Burley  1   2   3   4   5 , Charmi Bhikadiya  1   2 , Chunxiao Bi  4 , Sebastian Bittrich  4 , Henry Chao  1   2 , Li Chen  1   2 , Paul A Craig  6 , Gregg V Crichlow  1   2 , Kenneth Dalenberg  1   2 , Jose M Duarte  4 , Shuchismita Dutta  1   2   3 , Maryam Fayazi  1   2 , Zukang Feng  1   2 , Justin W Flatt  1   2 , Sai J Ganesan  7   8 , Sutapa Ghosh  1   2 , David S Goodsell  1   2   3   9 , Rachel Kramer Green  1   2 , Vladimir Guranovic  1   2 , Jeremy Henry  4 , Brian P Hudson  1   2 , Igor Khokhriakov  4 , Catherine L Lawson  1   2 , Yuhe Liang  1   2 , Robert Lowe  1   2 , Ezra Peisach  1   2 , Irina Persikova  1   2 , Dennis W Piehl  1   2 , Yana Rose  4 , Andrej Sali  7   8 , Joan Segura  4 , Monica Sekharan  1   2 , Chenghua Shao  1   2 , Brinda Vallat  1   2 , Maria Voigt  1   2 , Benjamin Webb  7   8 , John D Westbrook  1   2 , Shamara Whetstone  1   2 , Jasmine Y Young  1   2 , Arthur Zalevsky  7   8 , Christine Zardecki  1   2
Affiliations

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Stephen K Burley et al. Protein Sci. 2022 Dec.

Abstract

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

Keywords: Mol*; PDB; Protein Data Bank; RCSB Protein Data Bank; Worldwide Protein Data Bank; electron microscopy; macromolecular crystallography; micro-electron diffraction; nuclear magnetic resonance spectroscopy; open access.

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Conflict of interest statement

The authors declare no conflict of interest with this publication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Figures

FIGURE 1
FIGURE 1
PDB archival data metrics (as of July 2022). (a) Growth in archive (1976–2021). (b) Growth by structure experimental method annually 2000–2021 (macromolecular crystallography (MX), nuclear magnetic resonance spectroscopy (NMR), 3D electron microscopy (3DEM), and multiple methods). Resolution of all (c) macromolecular crystallography and (d) 3D electron microscopy structures
FIGURE 2
FIGURE 2
PDB data life cycle and RCSB PDB services. RCSB PDB hosts four integrated, interdependent cyberinfrastructure services, supported by a Customer Service Help Desk and an Infrastructure Team
FIGURE 3
FIGURE 3
The RCSB PDB research‐focused web portal home page (RCSB.org)
FIGURE 4
FIGURE 4
Structure Summary Page for PDB ID 5jxe. (a) Upper section hosts structure images, summary of structure contents, wwPDB Validation quality assessment, and primary literature citation. The link to the 1D‐3D viewer is highlighted with a red ellipse. (b) Macromolecules Section: First of three subsections providing detailed summary for the two copies of human PD‐1 present in the structure. (N.B.: Additional subsections for two copies each of the heavy and light chains of the pembrolizumab monoclonal antibody Fab are not shown.) “Find similar proteins by:” can be invoked for Sequence similarity searching (magenta ellipse) from a pull‐down menu to select desired percentage of sequence similarity. “Find similar proteins by:” can be invoked for 3D Structure similarity searching (red ellipse) with a single mouse click. The Entity Group Sequence Clusters 30% Identity search button is denoted with a magenta rectangle. (c) Experimental Data & Validation and Entry History Sections
FIGURE 5
FIGURE 5
1D‐3D View for PDB ID 5jxe. In the left panel, clicking on Ser55 (highlighted with a red arrow) on the track CHAIN A (at the top of the page) invokes 3D graphical display of the view on the right, showing a hydrogen bond between the sidechains of Ser55 of human PD‐1 (labeled Ser55) and Arg99 of the pembrolizumab Heavy Chain (not labeled). Atom color coding: O‐red; N‐blue, C‐green (for PD‐1), C‐yellow (for pembrolizumab Heavy Chain), and C‐pink (for pembrolizumab Light Chain)
FIGURE 6
FIGURE 6
Entity Group Sequence Clusters 30% Identity for human PD‐1. (a) Group Summary page, consisting of three components: ribbon representation drawings for individual Group Members with buttons provide access to the Structure Summary Pages (Summary) and a Mol* display (Structure); a graphical table showing Group Members; and bar‐graph summarizing public release dates for individual Group Members. (b) Group Sequence page, providing a multiple sequence alignment of Group Members. Additional tabs on the Group Sequence page provide access to information about Structural Features and Binding Sites
FIGURE 7
FIGURE 7
Advanced Search Query Builder used to combine Structure Attribute search for PDB structures containing human PD‐L1 (UniProt ID Q9NZQ7) with Chemical Attribute search for ligands with molecular weight between 300 and 1000 Da occurring is shown. The Options for returning Structure data and Molecular Definition data are highlighted
FIGURE 8
FIGURE 8
Superposition of PD‐1 proteins in the PDB IDs 5jxe and 4zqk created using Mol*. Ribbon representations of PD‐1 (bright green outline), PD‐L1 in PDB ID 4zqk (dark gray), and pembrolizumab Fab Heavy (gold) and Light (magenta) Chains. PD‐L1 and the Fab Heavy Chain cannot bind PD‐1 simultaneously because the two proteins would clash sterically (see labeled red arrow)
FIGURE 9
FIGURE 9
Artistic conception of VegF signaling from the Molecule of the Month article Vascular Endothelial Growth Factor (VegF) and Angiogenesis. Two neighboring cells are shown with cell membrane in green and cytoplasm in blue, and blood plasma at the top left in tan. VegF (magenta) arrives through the blood to the potential site of a new blood vessel and brings together two copies of VegF receptor (top center, lavender with glycosylation in yellow) to form an active dimer. Activated VegF receptor then initiates a signal cascade of kinases (yellow molecules attached to the membrane and pink molecules in the cytoplasm), leading to phosphorylation of many proteins, including cadherin (green). The phosphorylated cadherins separate making room for new blood vessels. Cytoplasmic proteins (blue) in the two cells include long actin filaments, L‐shaped tRNA, a small ribosomal subunit, and many metabolic enzymes. The full image is available at PDB‐101 (doi: 10.2210/rcsb_pdb/goodsell‐gallery‐041)
See this image and copyright information in PMC

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