PDBe: Protein Data Bank in Europe

Published online 21 November 2011 Nucleic Acids Research, 2012, Vol. 40, Database issue D445–D452 doi:10.1093/nar/gkr998 PDBe: Protein Data Bank in Europe S. Velankar, Y. Alhroub, C. Best, S. Caboche, M. J. Conroy, J. M. Dana, M. A. Fernandez Montecelo, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas, P. Haslam, P. M. S. Hendrickx, E. Heuson, M. Hirshberg, M. John, I. Lagerstedt, S. Mir, L. E. Newman, T. J. Oldfield, A. Patwardhan, L. Rinaldi, G. Sahni, E. Sanz-Garcı́a, S. Sen, R. Slowley, A. Suarez-Uruena, G. J. Swaminathan, M. F. Symmons, W. F. Vranken, M. Wainwright and G. J. Kleywegt* Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 23, 2011; Accepted October 18, 2011 ABSTRACT The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistryand taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi). INTRODUCTION Since the early 1970s, the Protein Data Bank (PDB) has been the single global archive in which 3D structure information about biomacromolecules (including complexes) is archived (1,2). Since 2003, the PDB archive has been managed by an international organization called the Worldwide PDB (wwPDB; wwpdb.org) (3,4). It consists of the Research Collaboratory for Structural Bioinformatics (RCSB) (5) and the BioMagResBank (BMRB) (6) in the USA, the Protein Data Bank Japan (PDBj) (7) and the Protein Data Bank in Europe (PDBe; pdbe.org) (8,9). The four wwPDB partners accept and process depositions of new structures and supporting experimental data and jointly curate, remediate and distribute the PDB archive. They also work together (often in consultation with the community) to define deposition and annotation policies and procedures, file formats, descriptions of chemical compounds and polymer components, and validation standards for structural data. In addition, each of the partners offers independent services to users of structural information. PDBe aims to develop tools, services and resources that help make the wealth of data about biomacromolecular structure and function more easily accessible to the wider biomedical community (10). Many of these tools have been described recently (8,9). In this article, we briefly describe several recently developed or enhanced services provided by PDBe. PDBportfolio: HIGHLIGHTING SALIENT FEATURES OF A PDB ENTRY In order to convey salient features and annotation in the context of 3D structure, PDBe has developed an animated widget called PDBportfolio (pdbe.org/portfolio), Figure 1. It presents a slide show of images that convey important information and value-added annotation about a selected PDB entry or entries. The legend of each image contains more details as well as links to relevant web pages at PDBe or external resources. The slide show covers: . Quaternary structure—the largest assembly identified by the depositors or PISA (11). . Deposited model—a cartoon and a surface representa- tion are shown separately. The cartoon is coloured by polymer chain and shown with non-polymeric entities as space-filling (CPK) models. The surface is coloured by atomic properties using some simple rules as defined in PyMol (pymol.org) (12). In the case of *To whom correspondence should be addressed. Tel: +44 1223 492698; Fax: +44 1223 494487; Email: ß The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. D446 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 1. The PDBportfolio widget provides images and annotation about important aspects of one or more PDB entries, including the quaternary structure, domains and bound ligands. Refer to the text and pdbe.org/portfolio for more information, or see pdbe.org/1fcc for a live animated example. protein–DNA/RNA complexes, the image shows only the protein surface for clarity. . Domain structure—separate images show SCOP (13), CATH (14) and Pfam (15) domains as annotated by the SIFTS resource (16). Each domain is highlighted using a coloured cartoon and its boundaries are further highlighted by a semi-transparent surface of the same colour. Different surface styles are used to distinguish multiple occurrences of the same domain type. . Ligands—the binding environment of at most three bound chemical compounds is shown. Compounds that are most likely crystallization agents (such as glycerol) are ignored. . Experiment-dependent information—for X-ray crystal structures, temperature-factor information is shown on the structure and red surface patches indicate where crystal contacts occur. For NMR entries, the entire ensemble of models is shown. For 3DEM entries, the Nucleic Acids Research, 2012, Vol. 40, Database issue D447 Figure 2. The UniPDB widget provides a graphical overview of the sequence coverage of any UniProt entry in the PDB. This example (pdbe.org/ unipdb?uniprot=FAS_HUMAN) shows the domain architecture of human fatty acid synthase (FAS), a multi-enzyme assembly line of fatty acids. Pfam identifies eight domains in human FAS, five of which have structural coverage in the PDB. Salient features of the relevant PDB entries are depicted using PDBlogos. Refer to the text and pdbe.org/unipdb for more information. EMDB (17,18) map is shown if available, with the PDB entry fitted into it. PDBportfolio is used to display information about every PDB entry on its PDBe Atlas page (e.g. pdbe.org/ 1cbs). The widget can also be used freely in external web pages to convey key information about one or more PDB entries. The control buttons on the interface allow users to manipulate the slide show. They may also download an archive with all the PDBportfolio images of an entry (as well as the PyMol scripts used to generate them), or view all images and legends in one web page. UniPDB: UniProt-PDB SEQUENCE COVERAGE UniPDB is a widget that provides a graphical display of the sequence coverage in the PDB of any UniProt (19) entry (pdbe.org/unipdb), Figure 2. Proteins encountered in PDB entries may contain partial sequences (e.g. one or more stably fo (...truncated)