RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’

Assessment of protein assembly prediction in CASP13

“…1 Protein function is linked and often is determined or regulated by the oligomeric structure. [2][3][4] As of March 2019, the average structure in the Protein Data Bank (PDB) 5 is a dimer and approximately half of the PDB is annotated as oligomeric. Estimates of the average protein oligomeric state in the cell point to an even higher tetrameric assembly.…”

Computer simulations of protein–membrane systems

“…Cryo-EM has in recent years become an important tool for investigating protein-lipid association in membranes systems with a resolution of 2-4 Å . 41 Every resolved protein structure is available in the RCBS Protein Data Bank (PDB) 42,43 (https://www.rcsb.org), while the orientation of membrane proteins in biological membranes is provided by the Orientations of Proteins in Membranes (OPM) database 44 (https://opm. phar.umich.edu/).…”

“…Membrane Builder provides a PDB loader, which at the starting step imports a protein structure from either the OPM 44 database or the RCBS PDB. 42,43 In the next step, the user can decide to use the whole or only part(s) of the loaded protein, for instance, only a certain chain or certain residues of each available chain. Furthermore, the protein structure can be modified by the PDB manipulator to introduce cap groups, mutations, disulfide bridges, unnatural amino acids, or posttranslational modifications, including glycosylation, lipidation for a lipid anchor, phosphorylation, or attachment of a GPI-anchor.…”

The LUFS domain, its transcriptional regulator proteins, and drug resistance in the fungal pathogen Candida auris

“…Modeling was performed by SWISS‐MODEL, using the crystal structure of SSBR2 as a template. The views are cartoons rendered by NGL Viewer on the RCSB PDB and SWISS‐MODEL web servers…”

“…Modeling was performed by SWISS-MODEL, 23 using the crystal structure of SSBR2 as a template. The views are cartoons rendered by NGL Viewer 24 on the RCSB PDB 25 and SWISS-MODEL web servers *"A mysterious infection, spanning the globe in a climate of secrecy" (April 6), "What you need to know about Candida auris" (April 6), "Candida auristhe fungus nobody wants to talk about" (April 8), "How a Chicago woman fell victim to Candida auris, a drug-resistant fungus" (April 17).…”