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JOINT USAGE / RESEARCH CENTERIPR Osaka University

JOINT USAGE / RESEARCH CENTER

ABOUT US

We aim to establish a core center for basic and applied research on proteins where we elucidate their structures and functions, and can understand their biological roles from molecular to cellular and higher levels. This will lead to marked advancements in life sciences in Japan.

To achieve this, we promote domestic and international collaborations, provide opportunities to access various facilities and databases, and organize IPR seminars. Through these activities, we help stimulate communities studying life sciences on the basis of proteins.

Our activities as a Joint Usage/Research Center are guided by the Administrative Council and Panel on Join Usage/Research, members of which are selected from external persons with relevant knowledge and experience, so that we can respond adequately to community trends.

Main Activities (of the Joint Usage and Research Center for Proteins)

  1. 01

    Joint usage of advanced facilities and equipment

    IPR offers the usage of its own synchrotron beamline at SPring-8, Nuclear Magnetic Resonance (NMR) spectrometers with ultra-high sensitivities and Cryo-electron microscopy at IPR, to domestic and international protein researchers.

  2. 02

    Access to databases

    IPR has developed a protein structural database (PDB: Protein Data Bank) as PDBj (PDB Japan), one of the four members of the wwPDB (worldwide PDB), by annotating the deposited data from structural biologists in Asia and Oceania and by providing several original services and derived databases. PDBj-BMRB is also constructing an NMR experimental database, collaborating with BMRB (BioMagResBank) in the U.S.A.

  3. 03

    Collaborations including those leading to the development of human resources

    Through public invitations to join the 7 collaborative programs above, we contribute to domestic and international communities devoted to protein sciences and the development of human resources.

Activities

Our major activities are to promote 1. Joint usage of advanced facilities and equipment, 2. Access to databases, and 3. Collaborations including those leading to the development of human resources. Through these activities, we aim to activate protein and life science communities.

  • Domestic Collaborators

  • International Collaborative Research

  • SPring-8 Collaborative Research

  • NMR Collaborative Research

  • Cryo-EM Collaborative Research

  • IPR Seminars

  • IPR Fellows

Organization

The Joint Usage/Research Centers on the basis of organization and advanced facilities of IPR

  • Collaborative Research
  • Joint usage of advanced facilities and equipment
  • Access to databases
  • IPR Divisions
    • Division of Protein Chemistry
    • Division of Protein Structural Biology
    • Division of Integrated Protein Functions
    • Division of Protein Network Biology
  • Research Center for Next-Generation Protein Sciences
  • 7 PublicInvitations

    1. 1Domestic Collaborators
    2. 2International Collaborative Research
    3. 3SPring8 Collaborative Research
    4. 4NMR Collaborative Research
    5. 5Cryo-EM Collaborative Research
    6. 6IPR Seminars
    7. 7IPR Fellows
    1. 1X-ray (SPring-8 and In-house)
    2. 2Mass
    3. 3EM
    4. 4NMR (solid / solution)
  • Free online access (pdbj.org etc.)

    Collaboration Research Facilities

    Collaboration with otherorganizations

Contribution to the communities studying life sciences on the basis of proteins

  • Collaborative Research
  • IPR Divisions
    • Division of Protein Chemistry
    • Division of Protein Structural Biology
    • Division of Integrated Protein Functions
    • Division of Multiscale Integrative Protein Science
  • Research Center for State-of-the-Art Functional Protein Analysis
  • 7 Public Invitations

    1. 1Domestic Collaborators
    2. 2International Collaborative Research
    3. 3SPring8 Collaborative Research
    4. 4NMR Collaborative Research
    5. 5Cryo-EM Collaborative Research
    6. 6IPR Seminars
    7. 7IPR Fellows

Contribution to the communities studying life sciences on the basis of proteins

  • Joint usage of advanced facilities and equipment
  • IPR Divisions
    • Division of Protein Chemistry
    • Division of Protein Structural Biology
    • Division of Integrated Protein Functions
    • Division of Multiscale Integrative Protein Science
  • Research Center for State-of-the-Art Functional Protein Analysis
    1. 1X-ray (SPring8)
    2. 2Mass
    3. 3EM
    4. 4NMR (solid / solution)
  • PDBj

    Collaboration Research Facilities

    Collaboration with otherorganizations

Contribution to the communities studying life sciences on the basis of proteins

  • Access to databases
  • IPR Divisions
    • Division of Protein Chemistry
    • Division of Protein Structural Biology
    • Division of Integrated Protein Functions
    • Division of Multiscale Integrative Protein Science
  • Research Center for State-of-the-Art Functional Protein Analysis
  • Free online access (pdbj.org etc.)

    Collaboration Research Facilities

    Collaboration with otherorganizations

Contribution to the communities studying life sciences on the basis of proteins

TOP-END FACILITIES

ⒸRIKEN

The state-of-the-art large experimental facilities housed in and operated by IPR cover all three major methodologies in the modern structural biology research field, namely, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

As for X-ray crystallography, we manage a contract beamline for macromolecular assemblies (BL44XU) at the SPring-8 synchrotron facility located in Nishi-Harima, Hyogo, ~120 km west from the institute. At the institute, as many as nine NMR spectrometers, including the flagship solution NMR model (950 MHz) and solid-state NMR equipped with an ultra-high sensitive DNP system, are housed and operated around the clock.

We also manage three cryo-EM scopes including Titan Krios (Thermo Fisher Scientific), Talos Arctica (Thermo Fisher Scientific), and JEM-2200FS (JEOL), all equipped with direct electron detector. They produce thousands of high-quality images every day to enable world-class single particle analyses for biologically important molecules.

Beamline for Biological Macromolecular Assemblies at SPring-8 (BL44XU)

The beamline for X-ray crystallography of biological macromolecules at SPring-8 (BL44XU) is available to researchers who belong to academic organizations throughout the world. Regular applications involving non-proprietary proposals are received once per year, and urgent applications can be accepted all year around. More than 50% of the total beamtime is used for collaborative research programs of the Institute for Protein Research. This beamline is specially designed for data collection of large unit cell crystals for analyzing biological macromolecular assemblies, such as protein complexes, protein-nucleic acid complexes, and viruses.

Year established

1999 (Upgraded in 2001, 2003, 2006, 2009, 2011, 2012, 2015, 2018)

Facility specification

Light source:
Undulator
Optics:
N2-cooled double crystal monochromator, Horizontal and vertical focusing mirrors
Detector:
Pixel array detector (Eiger 16M)

Solution NMR Spectrometer in an Ultra-high Magnetic Field

The ultra high field NMR instruments ( ¹H resonance frequency of 950 and 800 MHz) enable the analysis of 3D structures dynamics and interactions of high molecular-weight protein complexes and organic molecules at low concentrations, which markedly exceeds the performance of conventional spectrometers. This device provides one of the world’s highest magnetic fields, following a 1000 MHz spectrometer in France.

Year established

2010 (Upgraded in 2013 and 2014)

Equipments

950 and 800 MHz NMR Spectroscopy (BRUKER) Spectrometer:
Avance III 950, Avance III HD 800 (2013 upgraded)
Probe:
Triple resonance cryogenic probe  (1H,13C,15N)

Solid-state NMR Spectrometers

These spectrometers enable the analysis of the structures and functions of biomolecules in non-crystalline solid states, such as proteins in lipid bilayers and amyloid proteins. The two DNP-NMR spectrometers are equipped with gyrotrons generating high-power submillimeter waves and sample-rotation systems at cryogenic temperatures. Thereby, they generate hyper-polarization that provide the world’s highest performance in NMR sensitivity.

Year established

2001 (Upgraded in 2006 and 2013)

Equipment

500MHz, 700MHz Solid-State NMR Spectrometers
600MHz/396GHz Solid-State DNP-NMR Spectrometer
700MHz/461GHz Solid-State DNP-NMR Spectrometer

Cryo-electron Microscopes

Cryoelectron microscopy (Cryo-EM) method has become powerful technology to determine 3D structure of macromolecules and received the Novel Prize in Chemistry 2017. IPR has an excellent lineup of cyro-EM machines and related equipments, enabling high-performance and high-throughput analyses. Three main machines are all equipped with direct electron detector (DED), and we have achieved determination of 2.3Å resolution structure in early 2018.

Year extablished

2012 (Upgraded in 2015 and 2017)

Equipments

120kV H-7650(2010-)
200kV JEM-2200FS(2012-)
300kV Titan Krios G2(2015-)
200kV Talos Arctica(2017-)

Analytical Apparatus for Supra-biomolecules

Knowledge of the chemical structures of biomolecules is indispensable for understanding their biological functions and roles. However, since they are normally obtained in limited amounts and consisting of various molecules with diverse chemical properties, their structures are difficult to analyze with conventional methods. The analytical apparatus for supra-biomolecules is a tandem mass spectrometer (MS/MS) equipped with the electrospray ionization method. It allows the detection of biomolecules at sub-picomole levels, especially proteins, peptides, and sugar chains of glycoproteins, and is used for their structural analyses.

Year extablished

1991

Equipments

Q-TOF II (MS/MS)

High-performance X-ray Diffractometer

Three X-ray diffractometers with cryo-stream coolers for protein crystallography are mounted on two rotating anode X-ray generators.

Year established

2003 (Upgraded in 2011 and 2016)

Equipments

X-ray generator:
RIGAKU FR-E SuperBright™, Confocal VariMax Mirror
Detector:
RIGAKU XtaLAB SynergyCustom/R-axis IV++

ABI Procise 491 cLC

Amino acid sequence (primary structure) of a protein is an essential information for studying protein structure and function. Full-length amino acid sequences of proteins are easily obtained from the information of genome, however, proteins in the actual living system are sometimes truncated at N-terminus or/and C-terminus or modified by post-translational modification.

Therefore, chemical sequencing using Edman degradation method gives valuable sequence information. In addition, the amino acid sequences of proteins of a species without genome information must be directly analyzed with the protein samples themselves.

In the Institute for Protein Research (IPR), we have two protein sequencers (ABI Procise 491 cLC and Shimadzu PPSQ-53A) to analyze the N-terminal sequence of a protein or a peptide. We accept requests from outside IPR as commissioned analyses.

Year established

2002

Equipments

Applied Applied Biosystems Procise 491 cLC

Year established

2019

Equipments

Shimadzu PPSQ-53A

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 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 four partners; the RCSB PDB and BMRB in USA, the PDBj in Japan, and the PDBe in UK. PDBj is a founding member of the wwPDB and 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 activiy is supported by JST-NBDC and the MEXT grant of Joint Usage/Research allocated to IPR, Osaka University.)

    PDB

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  • 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 (PDBj-BMRB) 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

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  • Electron Microscopy Data Base(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

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  • Electron Microscopy Public Image Archive (EMPIAR)

    The Electron Microscopy Public Image Archive (EMPIAR) is a public resource for raw, 2D electron microscopy images. The office of EMPIAR is operated by European Bioinformatics Institute (EBI) in UK. PDBj started the branch office activity of distributing and brokering the EMPIAR data from 2017, collaborating with EBI. We are planning more activities, such as curating and processing the regional data, in our branch office in near future. (This activity is supported by AMED-BINDS)

    EMPIAR

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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.

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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.

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Adopted subjects/Reports

International Collaborative Research

The research results have to be reported within one month after completion of the collaborative research.

Please submit “(1)2019 Research Report Form” and “(2)2019 Summary of Research Report Form” to us by May 15, 2020.

*The forms are written in English.
*”(2)Summary of Research Report” will be published on this website.

The Synchrotron Radiation Beamline for Macromolecular Assemblies

Form can be downloaded from the web site.
www.protein.osaka-u.ac.jp/rcsfp/supracryst/en/research/beamline/

Users are required to submit an Experiment Summary Report online within 60 days after the end of each half-year research term. Publish your research in a refereed journal or equivalent (refereed proceedings dissertation, etc.) and register the publications with the Publications Database within three years after the end of the research term. It will be requested to include the sentence which shows the usage of the beamline in the publication, and send the reprint to Institute for Protein Research.

e.g. This work was performed using a synchrotron beamline BL44XU at SPring-8 under the Collaborative Research Program of Institute for Protein Research, Osaka University. Diffraction data were collected at the Osaka University beamline BL44XU at SPring-8 (Harima, Japan) (Proposal No. 2017BXXXX, 2018AXXXX, and 2018BXXXX).

INFORMATION

Accommodations for International Researchers

Information about Accommodations for International Researchers can be downloaded from the web site.
www.osaka-u.ac.jp/en/academics/facilities/BandB

CONTACT

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