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TOP-END FACILITIES

TOP-END FACILITIES

ⒸRIKEN

IPR operates state-of-the-art facilities for modern structural biology research, including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

As for X-ray crystallography, we operate a contract beamline (BL44XU) for macromolecular assemblies at the SPring-8 synchrotron facility, which is approximately 120 km west of IPR in Nishi-Harima, Hyogo. The institute houses and operates up to nine NMR spectrometers, including the flagship solution NMR model (950 MHz) and solid-state NMR with an ultra-highly sensitive DNP system, operating 24/7.

IPR also manages three cryo-EM scopes including Titan Krios (Thermo Fisher Scientific), Talos Arctica (Thermo Fisher Scientific), and JEM-2200FS (JEOL), all equipped with direct electron detectors capable of world-class high-resolution single-particle analysis and electron tomography.

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 X 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 1200 MHz spectrometer.
600, 500, and 400 MHz NMR instruments are also available, allowing structure, dynamics, and interaction analysis of proteins and small molecules to be conducted.

Year established

2010 (Upgraded in 2013, 2014 and 2020)

Equipments

950, 800, 600, 500, and 400 MHz NMR Spectroscopy (BRUKER) *
* TopSpin 3.6.2; Remote measurement is supported (2020 upgraded).
Spectrometer:
Avance III 950
Avance III HD 800, 600, 400 (2013 upgraded) Avance III HD 500 (2014 upgraded)
Probe:
CRYO TCI probe[950MHz]
CRYO TXI probe[800MHz]
CRYO QCI-P probe [600MHz]
CRYO BBO H/F probe [500 MHz]
BBFO, TXI probe [400MHz]
Sample changer:
SampleCaseCooled [600MHz] (2020 upgraded) SampleXpress [400MHz]

Ultra-High-Sensitivity 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

500 MHz Solid-State NMR Spectrometer
700 MHz Solid-State NMR Spectrometer
400MHz/263GHz Solid-State DNP-NMR Spectrometer
600MHz/396GHz Solid-State DNP-NMR Spectrometer
700MHz/461GHz Solid-State DNP-NMR Spectrometer

Cryo-electron Microscopes

IPR is equipped with cutting-edge cryo-electron microscopy instruments for the precise structural analysis of biological samples. In addition to the single-particle analysis for purified biomolecules, we cover all aspects of electron structural studies, including electron tomography for biomolecules in cells as well as microED for small molecules. IPR offers a complete range of equipment for sample preparation, such as a high-pressure freezing, a cryo-microtome, and a blot-free cryo-grid preparation robot, to meet diverse observation needs.

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-)

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

Protein sequencer (Shimadzu PPSQ-53A)

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.

Our protein sequencer, Shimadzu PPSQ-53A can analyze the N-terminal sequence of a protein or a peptide. We accept requests from outside IPR as commissioned analyses.

Year established

2019

Equipment

Shimadzu PPSQ-53A

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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 @)