PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Abstract

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.

Figure 1.

Screenshot from PDB Web pages for PDB entry 4IGK (structure of human BRCA1 BRCT in complex with ATRIP peptide, pdbe.org/4igk), showing SIFTS annotations from GO, Pfam, InterPro and CATH.

Figure 2.

Screenshot of interactive sequence (1D), topology (2D) and 3D structure components for the catalytic subunit of cAMP-dependent protein kinase (PDB entry 1ATP, pdbe.org/1atp).

Figure 3.

3D interactive visualisations of two instances of muramic acid in PDB structures of comparable resolution using LiteMol 3D viewer. (A) Data for entry 1LOD (pdbe.org/1lod) at 2.05 Å resolution. (B) Data for entry 5M1A (pdbe.org/5m1a) at 2.0 Å resolution. In both panels, electron density shown in blue mesh is where the experimental data and model agree (so called 2mFo-DFc map, plotted at contour level of 1.5σ, where σ is the standard deviation of the map), while electron density expected from the model and not present in the experimental data is shown in red mesh (negative values in mFo-DFc map, plotted at –3σ contour level), and electron density unexplained by the model is shown in green mesh (positive values in mFo-DFc map, plotted at +3σ contour).

Figure 4.

Examples showing summary and links to experimental data automatically fetched for (A) PDB entry 3J7L (pdbe.org/3j7l) from EMPIAR (B) PDB entry 5TOK (pdbe.org/5tok) from SBGrid Data Bank and (C) PDB entry 4WEQ (pdbe.org/4weq) from IRRMC.