PDBj

PDBj
Name	PDBj
Type	Research institution
Founded	2000
Location	Tokyo, Japan
Affiliation	Institute for Protein Research, Osaka University

PDBj PDBj is a structural biology data repository node that archives, curates, and disseminates macromolecular structure information. It provides integrated access to structural data for biomolecules, supports deposition workflows, and develops tools used by researchers, educators, and industry stakeholders. Operated within an academic environment, PDBj collaborates internationally to align with community standards and to integrate with computational and experimental resources.

Introduction

PDBj operates as a regional partner in the global structural biology infrastructure alongside RCSB Protein Data Bank, PDBe, BMRB, EMDB, EMPIAR, UniProtKB, and mmCIF initiatives. Located at the Institute for Protein Research, Osaka University, it serves users across Asia, working with institutions such as RIKEN, Tohoku University, Kyoto University, The University of Tokyo, and National Institute of Genetics. The organization participates in community governance with entities including the Worldwide Protein Data Bank organization, and aligns with standards developed by groups like International Union of Crystallography and Protein Data Bank in Europe (PDBe). Its remit spans crystal structure archives linked to experimental facilities such as SPring-8, SPring-8 Angstrom Compact Free Electron Laser, and cryo-EM centers like Osaka University Cryo-EM Facility.

Services and Resources

PDBj provides deposition interfaces comparable to systems used by RCSB Protein Data Bank and PDBe, and offers searchable archives interoperable with resources including UniProtKB, NCBI, EMDB, PubMed, and GenBank. It supplies downloadable coordinate files and validation reports adopted by journals such as Nature, Science, Cell, Proceedings of the National Academy of Sciences, and Journal of Molecular Biology. Educational portals link to datasets from structural studies involving targets like hemoglobin, ribosome, ATP synthase, G-protein coupled receptor, and RNA polymerase II. PDBj curates cross-references to biochemical databases including KEGG, ChEMBL, DrugBank, Pfam, and InterPro, facilitating multidisciplinary integration with projects such as AlphaFold, Rosetta, Phenix, and CryoSPARC.

Data Deposition and Curation

The deposition workflow supports authors from institutions such as University of Cambridge, Harvard University, Stanford University, Massachusetts Institute of Technology, University of Oxford, and Max Planck Society. Validation pipelines incorporate community metrics endorsed by organizations like International Union of Crystallography and tools such as MolProbity, phenix.refine, and REFMAC. Curators liaise with experimental facilities including Diamond Light Source, European Synchrotron Radiation Facility, Advanced Photon Source, and Argonne National Laboratory to reconcile metadata and experimental parameters. Data stewardship practices reflect policies advocated by funders like National Institutes of Health, European Research Council, Japan Society for the Promotion of Science, and publishers including Nature Publishing Group and Elsevier.

Tools and Software

PDBj develops web services, visualization tools, and APIs interoperable with software such as PyMOL, UCSF Chimera, VMD, Jmol, and Coot. Interactive viewers support volumetric maps from cryo-electron microscopy workflows and integrate with image-processing suites like RELION and CryoSPARC. Computational toolchains connect to modeling platforms including RosettaCM, MODELLER, and machine-learning models like AlphaFold. Programmatic access leverages standards from RESTful API practices and integrates with workflow managers used in labs at University of California, San Francisco, Weizmann Institute of Science, and ETH Zurich.

Collaborations and Partnerships

PDBj partners regionally and globally with nodes and consortia such as RCSB Protein Data Bank, PDBe, BMRB, EMDB, and research infrastructures like ELIXIR, JST, and NBDC. It engages with experimental centers including SPring-8, Spring-8 BL44XU, KEK Photon Factory, and international synchrotrons like ESRF and SOLEIL. Academic collaborations include departments and institutes at Osaka University, Kyoto University, Tohoku University, University of Tokyo, Kobe University, and Hokkaido University. Industry partnerships span biotechnology and pharmaceutical companies that use structural data from projects similar to Human Genome Project-scale initiatives and drug-discovery consortia including those tied to Structural Genomics Consortium.

Impact and Usage

PDBj data and services support research cited in high-impact journals such as Nature, Science, Cell, Nature Communications, and PNAS, and underpin studies involving macromolecular machines like ribosome, spliceosome, proteasome, DNA polymerase, and topoisomerase II. Its resources assist computational efforts at centers including RIKEN Center for Advanced Intelligence Project, J-PARC, Osaka University Graduate School of Medicine, and collaborations with consortia like Human Proteome Organization and International Cancer Genome Consortium. Educational outreach leverages examples from landmark structures determined by teams at Howard Hughes Medical Institute, Max Planck Institute for Biophysical Chemistry, and European Molecular Biology Laboratory. PDBj’s integration into the global data ecosystem enhances reproducibility and accelerates discovery in structural biology and related biomedical research.

Category:Biological databases Category:Structural biology