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Structural analysis of the intracellular proteolytic system

Planned Research

Project AreaProteolysis in the Regulation of Biological Processes
Project/Area Number 18076003
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

TOCHIO Hidehito (TOHCIO Hidehito)  Kyoto University, 大学院・工学研究科, 准教授 (70336593)

Co-Investigator(Kenkyū-buntansha) KURIMOTO Eiji  名古屋市立大学, 大学院・薬学研究科, 研究員 (90234575)
NODA Nobuo  北海道大学, 大学院・薬学研究科, 助教 (40396297)
YAMAGUCHI Yoshiki  理化学研究所, チームリーダー (90323451)
Project Period (FY) 2006 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥136,000,000 (Direct Cost: ¥136,000,000)
Fiscal Year 2010: ¥28,500,000 (Direct Cost: ¥28,500,000)
Fiscal Year 2009: ¥28,500,000 (Direct Cost: ¥28,500,000)
Fiscal Year 2008: ¥28,500,000 (Direct Cost: ¥28,500,000)
Fiscal Year 2007: ¥28,500,000 (Direct Cost: ¥28,500,000)
Fiscal Year 2006: ¥22,000,000 (Direct Cost: ¥22,000,000)
KeywordsX線結晶構造解析 / オートファジー / ユビキチン / NMR / 中性子小角散乱 / 構造生物学 / プロテアソーム / ユビキチン結合酵素 / At16 / 溶液NMR / Xさ洙結晶構造解析
Research Abstract

Structural studies of proteins and protein complexes related to the ubiquitin-proteasome system and autophagy were conducted using X-ray crystallography, NMR and small-angle neutron scattering techniques. The details of the ubiquitin interaction mode of ubiquitin receptors,the working mechanism of E2 (UbcH5b) and the activation mechanism of SCF E3 by NEDD8 were revealed. We also determined the structures of deconjugating enzyme Atg4B bound to LC3, E1-like enzyme Atg7, Atg12-Atg5 conjugate, and Atg8-Atg19 and LC3-p62 complexes, clarifying the molecular mechanisms of reversible Atg8 lipidation and autophagic receptor recognition byAtg8/LC3.

Report

(7 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report   Self-evaluation Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (113 results)

All 2011 2010 2009 2008 2007 2006 Other

All Journal Article (72 results) (of which Peer Reviewed: 65 results) Presentation (38 results) Remarks (3 results)

  • [Journal Article] Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip452010

    • Author(s)
      Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M.
    • Journal Title

      Proteins 78

      Pages: 1491-1502

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains.2010

    • Author(s)
      Morimoto D, Isogai S, Tenno T, Tochio H, Shirakawa M, Ariyoshi M.
    • Journal Title

      Acta Crystallograph Sect F Struct Biol Cryst Commun 66

      Pages: 834-837

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solution structure of a zinc-finger domain that binds to poly-ADP-ribose.2010

    • Author(s)
      Isogai S, Kanno S.I., Ariyoshi M, Tochio H, Ito Y, Yasui A, Shirakawa M.
    • Journal Title

      Genes Cells 15

      Pages: 101-110

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Distance Determination in Proteins inside Xenopus laevis Oocytes by Double Electron-Electron Resonance Experiments.2010

    • Author(s)
      Igarashi R, Sakai T, Hara H, Tenno T, Tanaka T, Tochio H, Shirakawa M.
    • Journal Title

      J Am Chem Soc 132

      Pages: 8228-8229

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] SANS investigation of assembly state of proteasome activator 28and the 20S proteasome.2010

    • Author(s)
      Sugiyama M, Kurimoto E, Sahashi H, Sakata E, Morimoto Y, Itoh K, Mori K, Fukunaga T, Minami Y, Kato K.
    • Journal Title

      J Phys Conf Ser 247

      Pages: 12020-12020

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates2010

    • Author(s)
      Sakata E, Satoh T, Yamamoto S, Yamaguchi Y, Yagi-Utsumi M, Kurimoto E, Tanaka K, Wakatsuki S, Kato K.
    • Journal Title

      Structure 18

      Pages: 138-147

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy.2010

    • Author(s)
      Fujioka Y, Noda NN, Nakatogawa H, Ohsumi Y, Inagaki F.
    • Journal Title

      J Biol Chem 285

      Pages: 1508-15

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The NMR structure of the autophagy-related protein Atg8.2010

    • Author(s)
      Kumeta K, Watanabe M, Nakatogawa H, Yamaguchi M, Ogura K, Adachi W, Fujioka Y, Noda NN, Ohsumi Y, Inagaki F.
    • Journal Title

      J Biomol NMR 47

      Pages: 237-241

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Atg8-family interacting motif crucial for selective autophagy.2010

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F.
    • Journal Title

      FEBS Lett 584

      Pages: 1379-1385

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway.2010

    • Author(s)
      Yamaguchi M, Noda NN, Nakatogawa H, Kumeta H, Ohsumi Y, Inagaki F.
    • Journal Title

      J Biol Chem 285

      Pages: 29599-29607

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34.2010

    • Author(s)
      Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F.
    • Journal Title

      J Biol Chem 285

      Pages: 30026-30033

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains2010

    • Author(s)
      Morimoto, D., Isogai, S., Tenno, T., Tochio, H., Shirakawa, M., Ariyoshi, M.
    • Journal Title

      Acta Crystallographica Section F

      Volume: 66 Pages: 834-837

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] H-1, C-13, and N-15 resonance assignment of the TIR domain of human MyD88.2010

    • Author(s)
      Ohnishi H, Tochio H, Kato Z, Kimura T, Hiroaki H, Kondo N, Shirakawa M.
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 4 Pages: 123-125

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distance Determination in Proteins inside Xenopus laevis Oocytes by Double Electron-Electron Resonance Experiments.2010

    • Author(s)
      Igarashi R, Sakai T, Hara H, Tenno T, Tanaka T, Tochio H, Shirakawa M.
    • Journal Title

      Journal of the American Chemical Society

      Volume: 132 Pages: 8228-8229

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solution structure of a zinc-finger domain that binds to poly-ADP-ribose2010

    • Author(s)
      Isogai, S., Kanno, S.I., Ariyoshi, M., Tochio, H., Ito, Y., Yasui, A., Shirakawa, M.
    • Journal Title

      Genes to Cells

      Volume: 15 Pages: 101-110

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Selective transport of alpha-mannosidase by autophagic pathways : structural basis for cargo recognition by Atg19 and Atg34.2010

    • Author(s)
      Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F
    • Journal Title

      Journal of Biological Chemistry

      Volume: 285 Pages: 30026-30033

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway.2010

    • Author(s)
      Yamaguchi M, Noda NN, Nakatogawa H, Kumeta H, Ohsumi Y, Inagaki F
    • Journal Title

      Journal of Biological Chemistry

      Volume: 285 Pages: 29599-29607

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The NMR structure of the autophagy-related protein Atg8.2010

    • Author(s)
      Kumeta H, Watanabe M, Nakatogawa H, Yamaguchi M, Ogura K, Adachi W, Fujioka Y, Noda NN, Ohsumi Y, Inagaki F
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 47 Pages: 237-241

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Atg8-family interacting motif crucial for selective autophagy2010

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F
    • Journal Title

      FEBS Letters

      Volume: 584 Pages: 1379-1385

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SANS investigation of assembly state of proteasome activator 28 and the 20S proteasome2010

    • Author(s)
      Masaaki Sugiyama
    • Journal Title

      J.Phys.Conf.Ser.

      Volume: 247 Pages: 12020-12020

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45.2010

    • Author(s)
      Sekiyama, N., Arita, R, Ikeda, Y., Hashiguchi, K., Ariyoshi, M., Tochio, H., Saitoh, H., Shirakawa. M.
    • Journal Title

      Proteins : Structure, Function, and Bioinformatics 78

      Pages: 1491-1502

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of UbcH5b ubiquitin intermediate : insight into the formation of the self-assembled E2 Ub conjugates.2010

    • Author(s)
      Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Tanaka, K., Wakatsuki, S., Kato, K
    • Journal Title

      Structure 18

      Pages: 138-147

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2.2009

    • Author(s)
      Tateishi Y, Ariyoshi M, Igarashi R, Hara H, Mizuguchi K, Seto A, Nakai A, Kokubo T, Tochio H, Shirakawa M.
    • Journal Title

      J Biol Chem 284

      Pages: 2435-2447

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling.2009

    • Author(s)
      Ohnishi H, Tochio H, Kato Z, Orii K.E., Li A.L., Kimura T, Hiroaki H, Kondo N, Shirakawa M.
    • Journal Title

      Proc Natl Acad Sci 106

      Pages: 10260-10265

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.2009

    • Author(s)
      Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H., Shirakawa M.
    • Journal Title

      Nature 458

      Pages: 106-109

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Assembly State of Proteasome Activator 28in an Aqueous Solution as Studied by Small-Angle Neutron Scattering2009

    • Author(s)
      Sugiyama M, Kurimoto E, Morimoto Y, Sahashi H, Sakata E, Hamada K, Itoh K, Mori K, Fukunaga T, Minami Y, Kato K.
    • Journal Title

      J Phys Soc Jpn 78

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.2009

    • Author(s)
      Satoo K, Noda NN(Co-first), Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F.
    • Journal Title

      EMBO J 28

      Pages: 1341-1350

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of Saccharomyces cerevisiae alpha-mannosidase, a cargo protein of the Cvt pathway.2009

    • Author(s)
      Watanabe Y, Noda NN, Honbou K, Suzuki K, Sakai Y, Ohsumi Y, Inagaki F.
    • Journal Title

      Acta Crystallograph Sect F Struct Biol Cryst Commun 65

      Pages: 571-573

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] ATG Systems from the Protein Structural Point of View.2009

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F.
    • Journal Title

      Chem Rev 109

      Pages: 1587-1598

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling.2009

    • Author(s)
      Ohnishi, H., Tochio, H., Kato, Z., Ori i, K. , Li, A., Kimura, T.
    • Journal Title

      Proceedings of the National Academy of Science 1260

      Pages: 10260-10265

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Assembly State of Proteasome Activator 28 in an Aqueous Solution as Studied by Small-Angle Neutron Scattering2009

    • Author(s)
      Sugiyama, M, Kurimoto, E., Morimoto, Y., Sahashi, H., Sakata, E., Hamada, K., Itoh, K., Mori, K., Fukunaga, T., Minami, Y., Kato, K.
    • Journal Title

      J.Phys.Soc.Jpn. 78(124802)

      Pages: 1-6

    • NAID

      130005437296

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ATG systems from the protein structural point of view.2009

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F
    • Journal Title

      Chem.Rev. 109

      Pages: 1587-1598

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autotihagy.2009

    • Author(s)
      Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F
    • Journal Title

      EMBO J. 28

      Pages: 1341-1350

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of Saccharomyces cerevisiae alpha-mannosidase, a cargo protein of the Cvt Dathway.2009

    • Author(s)
      Watanabe Y, Noda..NN, Honbou K, Suzuki K, Sakai Y, Ohsumi Y, Inagaki F
    • Journal Title

      Acta Crystallogr.Sect. F Struct.Biol.Cryst.Commun. 65

      Pages: 571-573

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of the Atgl7-Atg29-Atg3l complex specifically required for starvation-induced autophagy in Saccharomyces cerevisiae.2009

    • Author(s)
      Kabeya Y, Noda NN, Fujioka Y, Suzuki K, Inagaki F, Ohsumi Y
    • Journal Title

      Biochem.Biophys.Res.Commun. 389

      Pages: 612-615

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its funcional significance in2009

    • Author(s)
      Fujioka Y, Noda NN, Nakatogawa H, Ohcumi Y, Inagaki F
    • Journal Title

      J.Biol.Chem. 285

      Pages: 1508-1515

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.2009

    • Author(s)
      Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H, Shirakawa M.
    • Journal Title

      Nature 458

      Pages: 106-109

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy2009

    • Author(s)
      Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F
    • Journal Title

      The EMBO Journal

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ATG SYstems from the Protein Structural Point of View2009

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F
    • Journal Title

      Chemical Reviews 109

      Pages: 1587-1598

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SANS simulation of aggregated protein in aueous solution2009

    • Author(s)
      Masaaki Sugiyama, Kei Hamada, Koichi Kato, Eiji Kurimoto, Kenta Okamoto
    • Journal Title

      Nucl. Instrum. Methods Phys. Res. A 600

      Pages: 272-274

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution multi-dimensional NMR spectroscopy of proteins in human cells2009

    • Author(s)
      Kohsuke Inomata, et.al.
    • Journal Title

      Nature 458

      Pages: 106-109

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of the Small Ubiquitin-like Modifier (SUMO)-interacting Motif of MBD1-containing Chromatin-associated Factor 1 Bound to SUMO-3.2008

    • Author(s)
      Sekiyama N, Ikegami T, Yamane T, Ikeguchi M, Uchimura Y, Baba D, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M.
    • Journal Title

      J Biol Chem 283

      Pages: 35966-35975

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.2008

    • Author(s)
      Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M.
    • Journal Title

      Nature 455

      Pages: 818-821

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes.2008

    • Author(s)
      Yashiroda H, Mizushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Niwa S, Kasahara M, Kurimoto E, Sakata E, Takagi K, Suzuki A, Hirano Y, Murata S, Kato K, Yamane T, Tanaka K.
    • Journal Title

      Nature Struct Mol Biol 15

      Pages: 228-236

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] In vitro reconstitution of plant ATG8 and ATG12 conjugation systems essential for autophagy.2008

    • Author(s)
      Fujioka Y, Noda NN, Fujii K, Yoshimoto K, Ohsumi Y, Inagaki F.
    • Journal Title

      J Biol Chem 283

      Pages: 1921-1928

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free interface diffusion method.2008

    • Author(s)
      Noda NN, Fujioka Y, Ohsumi Y, Inagaki F.
    • Journal Title

      J Synchrotron Radiat 15

      Pages: 266-268

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of target recognition by Atg8/LC3 during selective autophagy.2008

    • Author(s)
      Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, Fujioka Y, Ohsumi Y, Inagaki F.
    • Journal Title

      Genes Cells 13

      Pages: 1211-1218

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of the coiled-coil domain of Atg16 essential for autophagy.2008

    • Author(s)
      Fujioka Y, Noda NN, Matsushita M, Ohsumi Y, Inagaki F.
    • Journal Title

      Acta Crystallograph Sect F Struct Biol Cryst Commun 64

      Pages: 1046-1048

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism2008

    • Author(s)
      Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M.
    • Journal Title

      Nature 455

      Pages: 818-821

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes.2008

    • Author(s)
      Yashiroda H, Mizushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Niwa S, Kasahara M, Kurimoto E, Sakata E, Takagi K, Suzuki A, Hirano Y, Murata S, Kato K, Yamane T, Tanaka K.
    • Journal Title

      Nature Struct. Mol. Biol. 15

      Pages: 228-236

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Structural basis of target recognition by Atg8/LC3 during selective autophagy2008

    • Author(s)
      Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, Fujioka
    • Journal Title

      Genes to Cells 13

      Pages: 1211-1218

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of the coiled-coil domain of Atg16 essential for autophagy2008

    • Author(s)
      Fujioka Y, NN, Matsushita M, Ohsumi Y, Inagaki F
    • Journal Title

      Acta Crystallographica Section F Structural Biology and Crystallization Communications 64

      Pages: 1046-1048

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free-interface diffusion method2008

    • Author(s)
      Noda NN, Fujioka Y, Ohsumi Y, Inagaki F
    • Journal Title

      Journal of Synchrotron Radiation 15

      Pages: 266-268

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] プロテアソームシャペロンX線結晶構造解析にとる26Sプロテアソームαリング形成機構の解析2008

    • Author(s)
      栗本英治,岡本健太、鈴木淳巨、日影達夫、山根隆、加藤晃一
    • Journal Title

      名古屋大学X線回折研究のあゆみ 29

      Pages: 3-6

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Hemi-methylated DNA recognition by the SRA protein Np95 via a base flipping mechanism2008

    • Author(s)
      Kyohei Arita, et.al.
    • Journal Title

      Natrue 455

      Pages: 818-821

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In vitro reconstitution of plant ATG8 and ATG12 conjugation systems essential for autophagy.2008

    • Author(s)
      Fujioka Y, Noda NN, Fujii K, Yoshimoto K, Ohsumi Y, Inagaki F.
    • Journal Title

      Journal of Biological Chemistry 283

      Pages: 1921-1928

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes.2008

    • Author(s)
      Yashiroda H, Mlzushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Niwa S, Easahara M, Kurimoto E, Sakate E, Takagi K.
    • Journal Title

      Nature struct. Mol. Biol. 15

      Pages: 228-236

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Paramagnetic relaxation-based 19F MRI probe to detect protease activity.2008

    • Author(s)
      Mizukami S, Takikawa R, Sugihara F, Hori Y, Tochio H, Walchli M, Shirakawa M, Kikuchi K.
    • Journal Title

      J Am Chem Soc. 130

      Pages: 794-5

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic and thermodynamic evidence for flipping of a methyl-CpG binding domain on2008

    • Author(s)
      Inomata K, Ohki I, Tochio H, Fujiwara K, Hiroaki H, Shirakawa M.
    • Journal Title

      Biochemistry 47

      Pages: 3266-71

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fbsl protects the malfolded glycoproteins from the attack of peptide:N-glycanase2007

    • Author(s)
      Yamaguchi Y, Hirao T, Sakata E, Kamiya Y, Kurimoto E, Yoshida Y, Suzuki T, Tanaka K, Kato K.
    • Journal Title

      Biochem Biophys Res Commun 362

      Pages: 712-716

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Direct interactions between NEDD8and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity2007

    • Author(s)
      Sakata E, Yamaguchi Y, Miyauchi Y, Iwai K, Chiba T, Saeki Y, Matsuda N, Tanaka K, Kato K
    • Journal Title

      Nature Struct Mol Biol 14

      Pages: 167-168

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy.2007

    • Author(s)
      Hanada T, Noda NN, Satomi Y, Ichimura Y, Fujioka Y, Takao T, Inagaki F, Ohsumi Y.
    • Journal Title

      J Biol Chem 282

      Pages: 37298-37302

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Direct interactions between NEDD8 and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity.2007

    • Author(s)
      E.Sakata, Y.Yamaguchi, Y.Miyauchi, K.Iwai, T.Chiba, Y.Saeki, N.Matsuda, K.Tanaka and K.Kato
    • Journal Title

      Nature Struct. Mol. Biol. 14

      Pages: 167-168

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] The Atgl2-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy.2007

    • Author(s)
      Hanada T, Noda NN, Satomi Y, Ichimura Y, Fujioka Y, Takao T, Inagaki F, Ohsumi Y.
    • Journal Title

      Journal of Biological Chemistry 282

      Pages: 37298-37302

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fbsl protects the malfolded glycoproteins from the attack of peptide: N-glycanase2007

    • Author(s)
      Yamaguchi Y, Hirao T, Sakata E, Kamiya Y, Kurimoto E, Yoshida Y, Suzuki T, Tanaka K, Kato K.
    • Journal Title

      Biochem. Biophys. Res. Commun 362

      Pages: 712-716

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Direct interactions between NEDD8 and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity2007

    • Author(s)
      E.Sakata, Y.Yamaguchi, Y.Miyauchi, K.lwai, T.Chiba, Y.Saeki, N.Matsuda, K.Tanaka, K.Kato
    • Journal Title

      Nature Struct.Mol.Biol. 14, 167-168 (2007) 14

      Pages: 167-168

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Structure of ATG5・ATG16, a complex essential for autophagy.2007

    • Author(s)
      Matsushita M, Suzuki NN, Obara K, Fujioka Y, Ohsumi Y, Inagaki F
    • Journal Title

      J Biol Chem 282

      Pages: 6763-6772

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The crystal structure of ATG3, an autophagy-related E2 enzyme that mediates ATG8 lipidation.2007

    • Author(s)
      Yamada Y, Suzuki NN, Hanada T, Ichimura Y, Kumeta H, Fujioka Y, Ohsumi Y, Inagaki F
    • Journal Title

      J Biol Chem 282

      Pages: 8036-8043

    • Related Report
      2006 Annual Research Report
  • [Journal Article] In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes.2006

    • Author(s)
      Sakai T, Tochio H, Tenno T, Ito Y, Kokubo T, Hiroaki H, Shirakawa M
    • Journal Title

      J Biomol NMR 36(3)

      Pages: 179-188

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Crystal structure of SUMO-3-modified thymine-DNA glycosylase.2006

    • Author(s)
      Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M
    • Journal Title

      J Mol Biol. 359(1)

      Pages: 137-147

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Evolutionally conserved intermediates between ubiquitin and NEDD82006

    • Author(s)
      R.Kitahara, Y.Yamaguchi, E.Sakata, Kasuya, K.Tanaka, K.Kato, S.Yokoyama, K.Akasaka
    • Journal Title

      J.Mol.Biol. 363

      Pages: 395-404

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.

    • Author(s)
      Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F
    • Journal Title

      The EMBO Journal in press

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Presentation] 中性子散乱によるPA28複合体およびα7ホモリングの動的高次構造解析2011

    • Author(s)
      栗本英治
    • Organizer
      日本薬学会第131年会
    • Place of Presentation
      静岡
    • Year and Date
      2011-03-29
    • Related Report
      2010 Final Research Report
  • [Presentation] 中性子小角散乱によるPA28αβ複合体およびα7ホモリングの動的高次構造解析2011

    • Author(s)
      栗本英治
    • Organizer
      日本薬学会 第131年会
    • Place of Presentation
      静岡
    • Year and Date
      2011-03-29
    • Related Report
      2010 Annual Research Report
  • [Presentation] オートファジー特異的PI3キナーゼ複合体の構造基盤2011

    • Author(s)
      野田展生
    • Organizer
      第6回オートファジー研究会
    • Place of Presentation
      掛川
    • Year and Date
      2011-01-12
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural basis of Atg8 activation and transfer to Atg3 by Atg72011

    • Author(s)
      Noda NN, Satoo K, Fujioka Y, Kumeta K, Ohsumi Y, Inagaki F.
    • Organizer
      Cold Spring Harbor Laboratory Meeting, The Ubiquitin Family
    • Place of Presentation
      Cold Spring Harbor, NY, USA.
    • Related Report
      2010 Final Research Report
  • [Presentation] Structural analysis of the UBA domain of p62 and its interaction with ubiquitin.2010

    • Author(s)
      Tochio H
    • Organizer
      Pacifichem 2010
    • Place of Presentation
      Hawaii Convention Center, Honolulu, USA.
    • Year and Date
      2010-12-18
    • Related Report
      2010 Final Research Report
  • [Presentation] 酵母Atg6/Vps30のTRECDの構造とオートファジーにおける役割2010

    • Author(s)
      Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F
    • Organizer
      BMB2010
    • Place of Presentation
      神戸
    • Year and Date
      2010-12-10
    • Related Report
      2010 Annual Research Report
  • [Presentation] p62UBAドメインの結晶構造とユビキチンとの相互作用2010

    • Author(s)
      杤尾豪人
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-17
    • Related Report
      2010 Final Research Report
  • [Presentation] Structural basis of selective autophagy.2010

    • Author(s)
      Noda NN
    • Organizer
      1^st Sino-Japan Symposium on Autophagy
    • Place of Presentation
      Xi'an, China.
    • Related Report
      2010 Final Research Report
  • [Presentation] Structural basis of selective autophagy.2010

    • Author(s)
      Noda NN
    • Organizer
      1st Sino-Japan Symposium on Autophagy
    • Place of Presentation
      Xi'an, China(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural Study of Complex Protein with Small-Angle Neutron Scattering2010

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      第48回 日本生物物理学会年会
    • Place of Presentation
      仙台
    • Related Report
      2010 Annual Research Report
  • [Presentation] p62 UBAドメインの結晶構造とユビキチンとの相互作用2010

    • Author(s)
      栃尾豪人
    • Organizer
      第10回 日本蛋白質科学会年会
    • Place of Presentation
      札幌(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural analysis of the UBA domain of p62 and its interaction with ubiquitin2010

    • Author(s)
      Hidehito Tochio
    • Organizer
      Pacifichem 2010
    • Place of Presentation
      Honolulu, USA(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] 重水素標識を利用した中性子小角散乱法によるプロテアソーム構成タンパク質PA28およびα7サブユニットの溶液構造解析2009

    • Author(s)
      栗本英治
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      2009-11-01
    • Related Report
      2010 Final Research Report
  • [Presentation] 重水素標識を利用した中性子小角散乱法によるプロテアソーム構成タンパクPA28およびα7サブユニットの溶液構造解析2009

    • Author(s)
      栗本英治, 佐橋広紀, 坂田絵理, 岡本健太, 南康文, 杉山正明, 加藤晃一
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島文理大学徳島キャンパス・アスティとくしま(徳島)
    • Year and Date
      2009-11-01
    • Related Report
      2009 Annual Research Report
  • [Presentation] Structural basis of cargo recognition during selective autoDhagy.2009

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F
    • Organizer
      International symposium on autophagy
    • Place of Presentation
      Otsu, Japan
    • Year and Date
      2009-09-25
    • Related Report
      2009 Annual Research Report
  • [Presentation] 中性子小角散乱を用いたプロテアソーム構成タンパク質の動的高次構浩解析2009

    • Author(s)
      栗本英治, 佐橋広紀, 坂田絵理, 岡本健太, 南康文, 杉山正明, 加藤晃一
    • Organizer
      第55回 日本薬学会東海支部総会・大会
    • Place of Presentation
      愛知学院大学(名古屋)
    • Year and Date
      2009-07-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] Structural basis of target recognition during selective autophagy2009

    • Author(s)
      Noda NN, Ohsumi Y, Inagaki F.
    • Organizer
      5^th International Symposium on Autophagy
    • Place of Presentation
      Otsu, Japan.
    • Related Report
      2010 Final Research Report
  • [Presentation] オートファジーに必須な出芽酵母Atg16の多量体ドメインのX 線構造解析2008

    • Author(s)
      藤岡優子、野田展生、松下美奈子、大隅良典、稲垣冬彦
    • Organizer
      第31回日本分子生物学会年会 第81回日本生化学会合同年会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-12
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] Cvt pathwayのレセプタータンパク質Atg19の構造生物学的研究2008

    • Author(s)
      渡辺康紀、野田展生、久米田博之、藤岡優子、鈴木邦律、大隅良典、稲垣冬彦
    • Organizer
      第31回日本分子生物学会年会第81回日本生化学会合同年会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2008-12-12
    • Related Report
      2008 Annual Research Report
  • [Presentation] オートファジーに必須な出芽酵母Atg16の多量体ドメインのX線構造解析2008

    • Author(s)
      藤岡優子、野田展生、松下美奈子、大隅良典、稲垣冬彦
    • Organizer
      第31回日本分子生物学会年会第81回日本生化学会合同年会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2008-12-12
    • Related Report
      2008 Annual Research Report
  • [Presentation] 第47回NMR討論会2008

    • Author(s)
      磯貝信, ほか10名
    • Organizer
      筑波大学
    • Place of Presentation
      筑波大学
    • Year and Date
      2008-11-14
    • Related Report
      2008 Annual Research Report
  • [Presentation] プロテアソームシャペロンX線結晶構造解析による26Sプロテアソームαリング形成機構の解析2008

    • Author(s)
      高木賢治, 水島恒裕, 八代田英樹, 岡本健太, 栗本英治, 山根隆, 田中啓二, 加
    • Organizer
      第72回日本生化学会中部支部例会
    • Place of Presentation
      岐阜薬科大学
    • Year and Date
      2008-05-24
    • Related Report
      2008 Annual Research Report
  • [Presentation] Structure and Interaction of Ubiquitin related Protein Domains:UBA and UBX2008

    • Author(s)
      Tochio H
    • Organizer
      Korea-Japan symposium on Biological NMR
    • Place of Presentation
      Seoul National University, Seoul, Korea
    • Year and Date
      2008-04-25
    • Related Report
      2010 Final Research Report
  • [Presentation] Crystal Structure and Biochemical Characterization of the UBA Domain of p62 (Sequestosome 1)2008

    • Author(s)
      Tochio H
    • Organizer
      ZOMES V:The Fifth International Symposium on the COP9 signalosome, Proteasome and eIF3: At the interface between signaling &proteolysis
    • Place of Presentation
      RIKEN Yokohama Institute,Yokohama, Japan.
    • Related Report
      2010 Final Research Report
  • [Presentation] Structural studies on the Atg12-Atg5oAtg16 complex essential for autophagy2008

    • Author(s)
      Noda NN, Matsushita M, Obara K, Fujioka Y, Ohsumi Y, Inagaki F.
    • Organizer
      Gordon Research Conference on Autophagy in Stress, Development & Disease
    • Place of Presentation
      entura, CA, USA.
    • Related Report
      2010 Final Research Report
  • [Presentation] Crystal structure of p62 ubiquitin associated (UBA) domain.2008

    • Author(s)
      Isogai S., Tenno T., Morimoto D., Abe S., Tochio H., Arita K., Ariyoshi M., Tanaka K., Shirakawa M.
    • Organizer
      IUCr 2008
    • Place of Presentation
      大阪
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] Crystal structure of p62 ubiquitin associated (UBA) domain2008

    • Author(s)
      磯貝信, ほか8名
    • Organizer
      IUCr2008
    • Place of Presentation
      Grand Cube Osaka、大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] 溶液中における単量体・二量体平衡にあるp62のユビキチン結合ドメインの解析2008

    • Author(s)
      森本大智, ほか8名
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] Crystallographic and NMR analyses of the novel 20S proteasome assembling chaperone PAC32007

    • Author(s)
      Kenta Okamoto, et. al.
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] ユビキチンリガーゼgp78とE2の相互作用のNMR解析2007

    • Author(s)
      武本映美
    • Organizer
      平成19年度日本薬学会東海支部会例会
    • Place of Presentation
      岐阜
    • Year and Date
      2007-12-08
    • Related Report
      2010 Final Research Report
  • [Presentation] 構造生物学的アプローチによる20Sプロテアソームサブユニットの集合過程の解析2007

    • Author(s)
      岡本健太, ら
    • Organizer
      平成19年度日本薬学会東海支部例会
    • Place of Presentation
      岐阜
    • Year and Date
      2007-12-08
    • Related Report
      2007 Annual Research Report
  • [Presentation] ユビキチンリガーゼgp78とE2の相互作用のNMR解析2007

    • Author(s)
      武本映美, ら
    • Organizer
      平成19年度日本薬学会東海支部例会
    • Place of Presentation
      岐阜
    • Year and Date
      2007-12-08
    • Related Report
      2007 Annual Research Report
  • [Presentation] 細胞表層における糖鎖認識の構造基盤:超高磁場NMRと糖鎖ライブラリーによるアプローチ2007

    • Author(s)
      加藤晃一, ら
    • Organizer
      第29回生体膜と薬物の相互作用シンポジウム
    • Place of Presentation
      仙台
    • Year and Date
      2007-11-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] 20SプロテアソームのアッセンブリーシャペロンPAC3の結晶構造2007

    • Author(s)
      岡本健太
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2007-05-26
    • Related Report
      2010 Final Research Report
  • [Presentation] 20SプロテアソームのアッセンブリーシャペロンPAC3の結晶構造2007

    • Author(s)
      岡本健太, 栗本英治, 坂田絵理, 鈴木淳巨, 山根隆, 平野祐子, 村田茂穂, 田中啓二, 加藤晃一
    • Organizer
      第7回日本蛋白質科学会年会
    • Year and Date
      2007-05-26
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] 20SプロテアソームのアッセンブリーシヤペロンPAC3の結晶構造2007

    • Author(s)
      岡本健太, ら
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2007-05-26
    • Related Report
      2007 Annual Research Report
  • [Presentation] NMR法を用いたHOIL-1LのUblドメインの立体構造解析2007

    • Author(s)
      三村俊介
    • Organizer
      日本薬学会第127年会
    • Place of Presentation
      富山
    • Year and Date
      2007-03-30
    • Related Report
      2010 Final Research Report
  • [Presentation] In-Cell NMR Spectroscopy of Proteins inside Xenopus laevis Oocytes2007

    • Author(s)
      Tochio H., Sakai T., Tenno T., Tanaka T., Hiroaki H., Shirakawa
    • Organizer
      48th Experimental NMR conference
    • Place of Presentation
      Daytona Beach, USA
    • Related Report
      2007 Annual Research Report
  • [Remarks] ホームページ等

    • URL

      http://www.rinshoken.or.jp/ER/PRBP/index.html

    • Related Report
      2010 Final Research Report
  • [Remarks] 京大グループの論文(5)の成果が以下の新聞にて報道された。京都新聞(3月5日26面)、科学新聞(3月13日1面)、日刊工業新聞(3月5日24面)および読売新聞(3月5日3面)および朝日新聞(4月3日13面)

    • Related Report
      2008 Self-evaluation Report
  • [Remarks] 京大グループの研究成果

    • URL

      http://www.kyoto-u.ac.jp/ja/news_data/h/h1/news6/2008/090305_2.htm

    • Related Report
      2008 Annual Research Report

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Published: 2006-04-01   Modified: 2018-03-28  

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