Protein Structure Database with new web services for structural biology and biomedical research

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Briefings in Bioinformatics (Impact Factor: 9.62). 08/2008; 9(4):276-85. DOI: 10.1093/bib/bbn015
Source: PubMed


The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.

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    • "ICD, intracellular domain; DD, death domain; DED, death effector domain; FADD, Fas-associated death domain protein. Figure 2 An example of the three-dimensional structure concerning a death ligand – death receptor complex revealed by crystallographic analysis Only the main chains within one-third of the complex (human LTα – human TNFR1 extracellular domain; cited and modified from an entry in Protein Data Bank Japan (PDBj) [124], 1tnr) are shown. Figure 3 Organization of the structural parts in human Fas ligand and human "
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    ABSTRACT: The extracellular domains of death ligands and those of death receptors are closely related to many serious human diseases through the initiation of apoptosis. Recombinant production of the extracellular domains has been investigated due to demand for a large amount of purified samples, which are a prerequisite for their biochemical characterization and constitute the fundamentals of medical applications. This review focuses on the recombinant production of extracellular domains of the major members of death ligand and death receptor families using non-mammalian expression systems with an emphasis on Fas ligand and Fas receptor. In contrast to the efficient production of the functional extracellular domains of TRAIL, TNFα and LTα by intracellular expression systems using Escherichia coli or Pichia pastoris, that of Fas ligand requires the secretory expression systems using P. pastoris or Dictyostelium discoideum, and the productivity in P. pastoris was largely dependent on tag sequence, potential N-glycosylation site and expressed protein region. On the other hand, the exploitation of insect cell systems is generally useful for the preparation of functional extracellular domains of death receptors containing many disulfide bridges in the absence of extended secondary structure, and a Bombyx mori larvae secretion system presented a superior productivity for human Fas receptor extracellular domain. Based on the results obtained so far, further efforts should be devoted to the artificial control of death ligand - death receptor interactions in order to make a contribution to medicine, represented by the development of novel biopharmaceuticals.
    Protein and Peptide Letters 04/2012; 19(8):867-79. DOI:10.2174/092986612801619606 · 1.07 Impact Factor
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    • "(2), the international partnership that manages the Protein Data Bank (PDB) (3,4) archive of experimentally determined biomacromolecular structures. The other wwPDB partners are the Research Collaboratory for Structural Bioinformatics (RCSB) (5) and the BioMagResBank (BMRB) (6) in the USA, as well as the Protein Data Bank Japan (PDBj) (7). The four partners provide data deposition and annotation facilities for the experimental structural-biology community. "
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    ABSTRACT: The Protein Data Bank in Europe (PDBe; is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration--it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.
    Nucleic Acids Research 11/2010; 39(Database issue):D402-10. DOI:10.1093/nar/gkq985 · 9.11 Impact Factor
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    • "When there is a crystal structure available for the protein, the PDB code ID (3) is included, as are hyperlinks to that entry at all three archiving sites—the RCSB (5), PDBj (6) and PDBe (7) websites. The reason for all three links is that each of the PDB sites has unique and complementary information and means of displaying and querying the data, and we believe easy access to all of them will benefit PCDDB users. "
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    ABSTRACT: The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at:
    Nucleic Acids Research 11/2010; 39(Database issue):D480-6. DOI:10.1093/nar/gkq1026 · 9.11 Impact Factor
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