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The Protein Data Bank in Europe (PDBe): bringing structure to biology - PubMed

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Sameer Velankar et al. Acta Crystallogr D Biol Crystallogr. 2011 Apr.

Abstract

The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

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Figures

**Figure 1**
The new PDBe home page, where the top search bar provides a common interface for simple searches of both PDB and EMDB. The ‘Quick access’ panel allows users to perform the most common tasks such as finding detailed information about a particular PDB entry, searching the PDB by various database identifiers or searching the PDB based on a protein sequence. The menu on the left provides access to many of the PDBe search and browse tools.

**Figure 2**
Example of an Atlas page, in this case for PDB entry
1lyz
. The menu on the left-hand side enables navigation between different areas of information and provides links to other resources and downloadable files. The main panel on the right shows the summary information for the entry.

**Figure 3**
PDBlogos and PDBprints. (a) PDBlogos are stylized icons that convey important information about a PDB entry. For example, these two PDBlogos signify that the biomacromolecule in an entry derives from a fungus and that the structure was determined by X-ray crystallography, respectively. (b) By default, PDBlogos are shown on a green background (although this may be set to a different colour on external websites). However, sometimes the background will be grey: this signifies that either the feature symbolized by the PDBlogo is absent or that the underlying data are not available, not published or not deposited. For instance, these two PDBlogos show that an entry does not contain any nucleic acid molecules and that the structure has not (yet) been published, respectively. (c) A PDBprint for a PDB entry is a collection of PDBlogos displayed in a specific order, where each icon represents a well defined category of information (see text). This PDBprint shows immediately that PDB entry
1cbs
is a published crystal structure of a heterologously expressed human protein in complex with a ligand for which the experimental diffraction data have beeen deposited. To help users familiarize themselves with the meaning of PDBlogos, tool tips are presented.

**Figure 4**
The PDBe enzyme-browser tool. The left-hand panel shows the EC classification as a tree and the right-hand panel gives detailed information on the selected class of enzyme. The central panel shows structure data relevant to the selected EC class organized as a number of tabs (*e.g.* ligands, quaternary structure, folds *etc*.).

**Figure 5**
The PDBe browser for analysing the results of sequence searches against the PDB. The query sequence can be shown aligned with each of the target sequences, together with their secondary structure, Pfam and CATH domain annotations.

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The Protein Data Bank in Europe (PDBe): bringing structure to biology - PubMed