PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education

Abstract

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.

Keywords: bioinformatics; databases; protein data bank; structural biology.

FIGURE 1

Overview of the infrastructure developed by the PDBe team The main wwPDB deposition system (OneDep) captures the core PDB data from depositors worldwide (light green). We enrich the core PDB data with annotations provided by PDBe‐KB partner databases and archive the data in internal databases (dark green). Finally, we provide data‐access mechanisms and visualizations for every aspect of the structural data we manage (red). PDBe, Protein Data Bank in Europe; PDBe‐KB, PDBe Knowledge Base; wwPDB, Worldwide Protein Data Bank

FIGURE 2

Example of using the PDBe graph database. The PDBe graph database is a powerful tool for research and discovery. In the example above, we queried the graph to identify ligand molecules in the PDB archive that bind to the same binding site and have the same molecular scaffolds. One of the ligand pairs matching this query is clarithromycin and erythromycin, a pair of antibiotics. Both molecules interact with the same amino acids of aminoglycoside phosphotransferase, for example with residue ILE105. These interactions can be viewed at https://www.ebi.ac.uk/pdbe/pdbe‐kb/proteins/Q47396/ligands. PDBe, Protein Data Bank in Europe

FIGURE 3

PDBe Mol*, PDBe ProtVista and the protein topology viewer The three main data‐visualization tools as displayed on the PDBe entry page of PDB 1KPA at https://www.ebi.ac.uk/pdbe/entry/pdb/1kpa/protein/1, corresponding to the human HINT1 protein. PDB ProtVista is at the top, the 2D topology viewer is at the bottom left, and PDBe Mol* is at the bottom right. Using these data‐visualization tools, users can do visual analyses, for example, examining the potential effect of a known mutation at LYS92. It becomes apparent that this residue is in a loop region that is part of the dimeric interaction interface. Therefore, one can speculate that a mutation might disrupt or destabilize the dimerization of HINT1. PDBe, Protein Data Bank in Europe

FIGURE 4

Bulk‐data download service We provide a bulk‐data download service for all aspects of PDB data. Using a list of PDB entries or small molecule identifiers (HET codes), users can retrieve large volumes of data from coordinate files to validation data and more. PDB, Protein Data Bank

FIGURE 5

PDBe‐KB aggregated views of proteins The latest update of the PDBe‐KB aggregated views of proteins offers a streamlined user experience with better separation and description of the various data we provide access to. Each primary section, such as “structures,” “ligands,” etc. has its own subpage. This allowed us to fine‐tune the performance of the subpages while also displaying more data before. The example shown here is the Replicase polyprotein 1ab of SARS‐CoV‐2, https://pdbe‐kb.org/proteins/P0DTD1. PDB, Protein Data Bank; PDBe‐KB, PDBe Knowledge Base