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DATABASE

Institute for Protein Research manages the six world standard databases (CSD, PDB, BMRB, EMDB, EMPIAR and MOUSE BASEMENT MEMBRANE BODYMAP) as a public good, covering the wide range of molecular size from the small molecular organic compounds and protein molecules to the extracellular matrix, and containing diverse data, such as chemical spectra, atomic coordinates of molecular structure and micrographs. Our databases provide additional links to other experimental database, journals and archives of chemical compounds, which is regarded as a core data resource for supporting the fundamentals of frontier biosciences.

PDBj (Protein Data Bank Japan) maintains global structural databases of macromolecular structures (the PDB, BMRB and EMDB core archives) and provides integrated tools and services, in collaboration with RCSB PDB and BMRB in the USA, and PDBe and EMDB in Europe.

  • Protein Data Bank(PDB)

    Protein Data Bank (PDB) is a single global archive of the experimentally determined structures of biological macromolecules. The PDB core archive is maintained by the worldwide PDB consortium with five partners; the RCSB PDB and BMRB in the USA, the PDBj in Japan, and the PDBe and EMDB in the UK. PDBj is a founding member of the wwPDB and is currently processing all the depositions originated from Asia and Middle East. From Osaka University, PDBj is distributing all PDB data to the world (https://pdbj.org). (This activity is supported by JST-NBDC and the MEXT grant of Joint Usage/Research allocated to IPR, Osaka University.)

    PDB

    WEBSITE

  • Biological Magnetic Resonance Data Bank (BMRB)

    The Biological Magnetic Resonance Data Bank (BMRB) is a repository for data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules. The head office of BMRB is located in USA, but PDBj is operating a branch office of BMRB based on the academic exchange agreement. The BMRB branch office at PDBj (BMRBj) is accepting and processing all the data deposited to the server machines installed at PDBj. All released data are available from our BMRB server to the world. (This activity is supported by JST-NBDC)

    BMRB

    WEBSITE

  • Electron Microscopy Data Bank(EMDB)

    The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. The deposited data from Asia and middle-East are processed by PDBj, and all other regional entries processed by other partner sites are collaboratively released to the world. EMDB entries with low resolution does not accompany the atomic coordinates, but those with high resolution may accompany the atomic coordinates, which is stored in the PDB archive. (This activity is supported by AMED-BINDS)

    EMDB

    WEBSITE

  • Electron Microscopy Public Image Archive (EMPIAR)

    The Electron Microscopy Public Image Archive (EMPIAR)is a public resource for raw, 2D electron microscopy images. EMPIAR is headquartered at the European Bioinformatics Institute (EBI), established by the European Molecular Biology Laboratory (EMBL) in the UK. PDBj began distributing and brokering the EMPIAR data from 2017 as a branch office, collaborating with EBI. We are responsible for curating and processing the regional data from Asia and disseminating single-particle cryo-EM image data from Osaka University to the world. (This activity is supported by AMED-BINDS.)

    EMPIAR

    WEBSITE

The Cambridge Structural Database (CSD).

The Cambridge Structural Database (CSD)

The Cambridge Structural Database (CSD) is one of the first numerical scientific databases in the world containing crystal structure data for all small molecules studied by X-ray or Neutron diffraction. The data have been archived from 1965 by the Cambridge Crystallographic Data Centre (CCDC) with continuing help from the crystallographic community worldwide. The first releases of the CSD System to the USA, Italy and Japan occurred in 1970’s and the Institute for Protein Research was in charge of distribution in Japan. Now, the CSD System is made available to academic users through the National Affiliated Centres (NACs), who undertake licensing and distribution of the media on the CCDC’s behalf in a specific country. Institute for Protein Research, Osaka University, is the NAC in Japan.

WEBSITE

Immunohistochemical database for basement membrane proteins

Immunohistochemical database for basement membrane proteins

Many cell types in our body sustain their functions through adhesive interactions with a sheet-like extracellular matrix called “basement membrane”. This database compiles high-resolution immunohistochemical images for a total of 42 basement membrane proteins including all subunit chains of laminins, collagen IV, and heparan sulfate proteoglycans (perlecan, agrin, and collagen XVIII) in mouse embryos. One can move around on a virtual slide of a whole mouse embryo and magnify any part of the embryo to locate basement membrane proteins of interest at a single cell level.

WEBSITE

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CONTACT

Project Team of Joint Usage / Research Center,
Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN

  •                                                               E-mail: tanpakuken-kyoten[at]office.osaka-u.ac.jp (change [at] to @)