Laboratory of Protein Databases (Protein Data Bank Japan)

At Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, we maintain databases involved in life science such as PDBj (Protein Data Bank Japan). The target databases are described below:


PDBj (Protein Data Bank Japan) is a partner to manage PDB, which includes molecular structural information of biological macromolecular such as proteins, and EMDB (Electron Microscopy Data Bank), which includes Coulomb potential maps obtained by electron cryo-microscopy. Under wwPDB (World Wide Protein Data Bank), we collaborate with RCSB PDB and BMRB in the USA, PDBe and EMDB in the EU, in the USA to manage the worldwide unique PDB/EMDB.

In Japan, we facilitate on utilizing life science databases collaborating with DBCLS (Data Base Center for Life Science) and DDBJ (DNA Data Bank Japan) under the support of 1. To promote this activity, we founded a common work framework JBI (Japan alliance for Bioscience Information).


BMRB (Biological Magnetic Resonance data Bank) is a database including various information about biomolecules studied by NMR (Nuclear Magnetic Resonance). Under the support of 1, we collaborate with the group in the University of Connecticut to accept deposition, develop various tools and maintain the Japan site of BMRB.


EMPIAR (Electron Microscopy Public Image ARchive), managed by EBI (European Bioinformatics Institute), is the raw image database to construct molecular structural information studied by electron microscopy. In 2018, we started to provide a mirror site of EMPIAR at Japan under the support of 2.

Biological Structure Model Archive (BSM-Arc, BSMA)BSMA

Biological Structure Model Archive (BSM-Arc, BSMA) is an archive to collect data obtained via in-silico methods related to structural biophysics (such as structure models or simulations).

X-Ray Diffraction Archive (XRDa)XRDa

X-Ray Diffraction Archive (XRDa) is the archive of raw X-ray diffraction images corresponding to PDB entries.

  1. "JST-NBDC" (Database Integration Coordination Program (DICP), Department of NBDC Program, Japan Science and Technology Agency) and "the MEXT grants for joint usage and research center assigned to Institute for Protein Research (IPR), Osaka University"
  2. BINDS (Basis for Supporting Innovative Drug Discovery and Life Science Research)


April 1st 2011
The database management group was separated from the Laboratory of Protein Infomatics (Professor Haruki Nakamura) to be founded the Laboratory of Protein Databases (Professor Haruki Nakamura).
April 1st 2018
With the retirement of Professor Haruki Nakamura, the head of the laboratory was replaced by Professor Genji Kurisu.
October 1st 2020
Along with the reorganization of IPR, the name of the laboratory was changed to "Protein Data Bank Japan".
July 1st 2023
Along with the reorganization of IPR, the name of the laboratory was changed to "Laboratory of Protein Databases".