PDBTM: Protein Data Bank of transmembrane proteins after 8 years

Abstract

The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous ‘exotic’ transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4

“…formed structural alignments between the model and all known crystal structures of membrane proteins, in the Protein Data Bank of Transmembrane Proteins), using TM-align (30,31,37). The hZIP4 dimeric model is closest in structure to MFS transporters (Fig.…”

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

Expression and purification of integral membrane metallopeptidase HtpX

“…Accordingly, in recent years much effort has been made to find expression systems that yield sufficient amounts of native-like protein and detergents/lipids that mimic the native membrane environment [3,4]. Nevertheless, IM proteins are still dramatically under-represented in the three-dimensional structural database of the Protein Data Bank (PDB; see http://www.pdb.org/ and [5]). …”