Structural analysis of the intracellular proteolytic system

• Project Area: Proteolysis in the Regulation of Biological Processes
• Project/Area Number: 18076003
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto 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: ¥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)
• Keywords: X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.

Research Products

• [Journal Article] Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45 (2010)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 Crystallographica Section F Volume: 66 Pages: 834-837
  • 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
  • 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
  • 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 to Cells Volume: 15 Pages: 101-110
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Atg8-family interacting motif crucial for selective autophagy (2010)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F
  • Journal Title: FEBS Letters Volume: 584 Pages: 1379-1385
  • Peer Reviewed
• [Journal Article] SANS investigation of assembly state of proteasome activator 28 and the 20S proteasome (2010)
  • Author(s): Masaaki Sugiyama
  • Journal Title: J.Phys.Conf.Ser. Volume: 247 Pages: 12020-12020
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Assembly State of Proteasome Activator 28in an Aqueous Solution as Studied by Small-Angle Neutron Scattering (2009)
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Assembly State of Proteasome Activator 28 in an Aqueous Solution as Studied by Small-Angle Neutron Scattering (2009)
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its funcional significance in (2009)
  • Author(s): Fujioka Y, Noda NN, Nakatogawa H, Ohcumi Y, Inagaki F
  • Journal Title: J.Biol.Chem. 285 Pages: 1508-1515
  • 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
  • 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, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F
  • Journal Title: The EMBO Journal
  • Peer Reviewed
• [Journal Article] ATG SYstems from the Protein Structural Point of View (2009)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F
  • Journal Title: Chemical Reviews 109 Pages: 1587-1598
  • Peer Reviewed
• [Journal Article] SANS simulation of aggregated protein in aueous solution (2009)
  • Author(s): Masaaki Sugiyama, Kei Hamada, Koichi Kato, Eiji Kurimoto, Kenta Okamoto
  • Journal Title: Nucl. Instrum. Methods Phys. Res. A 600 Pages: 272-274
  • Peer Reviewed
• [Journal Article] High-resolution multi-dimensional NMR spectroscopy of proteins in human cells (2009)
  • Author(s): Kohsuke Inomata, et.al.
  • Journal Title: Nature 458 Pages: 106-109
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Journal Title: Genes to Cells 13 Pages: 1211-1218
  • Peer Reviewed
• [Journal Article] Crystallization of the coiled-coil domain of Atg16 essential for autophagy (2008)
  • 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
  • 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: Journal of Synchrotron Radiation 15 Pages: 266-268
  • 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
• [Journal Article] Hemi-methylated DNA recognition by the SRA protein Np95 via a base flipping mechanism (2008)
  • Author(s): Kyohei Arita, et.al.
  • Journal Title: Natrue 455 Pages: 818-821
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Kinetic and thermodynamic evidence for flipping of a methyl-CpG binding domain on (2008)
  • Author(s): Inomata K, Ohki I, Tochio H, Fujiwara K, Hiroaki H, Shirakawa M.
  • Journal Title: Biochemistry 47 Pages: 3266-71
  • Peer Reviewed
• [Journal Article] Fbsl protects the malfolded glycoproteins from the attack of peptide:N-glycanase (2007)
  • 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
  • Peer Reviewed
• [Journal Article] Direct interactions between NEDD8and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity (2007)
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Fbsl protects the malfolded glycoproteins from the attack of peptide: N-glycanase (2007)
  • 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
  • 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.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
• [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
• [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
• [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
• [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
• [Journal Article] Evolutionally conserved intermediates between ubiquitin and NEDD8 (2006)
  • 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
• [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
  • 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
• [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
• [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
• [Presentation] Structural basis of Atg8 activation and transfer to Atg3 by Atg7 (2011)
  • 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.
• [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
• [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
• [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
• [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.
• [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)
• [Presentation] Structural Study of Complex Protein with Small-Angle Neutron Scattering (2010)
  • Author(s): Masaaki Sugiyama
  • Organizer: 第48回 日本生物物理学会年会
  • Place of Presentation: 仙台
• [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)
• [Presentation] Structural analysis of the UBA domain of p62 and its interaction with ubiquitin (2010)
  • Author(s): Hidehito Tochio
  • Organizer: Pacifichem 2010
  • Place of Presentation: Honolulu, USA(招待講演)
• [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
• [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
• [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
• [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
• [Presentation] Structural basis of target recognition during selective autophagy (2009)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F.
  • Organizer: 5^th International Symposium on Autophagy
  • Place of Presentation: Otsu, Japan.
• [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
• [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
• [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
• [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
• [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
• [Presentation] Structure and Interaction of Ubiquitin related Protein Domains:UBA and UBX (2008)
  • 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
• [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.
• [Presentation] Structural studies on the Atg12-Atg5oAtg16 complex essential for autophagy (2008)
  • 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.
• [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
• [Presentation] Crystal structure of p62 ubiquitin associated (UBA) domain (2008)
  • Author(s): 磯貝信, ほか8名
  • Organizer: IUCr2008
  • Place of Presentation: Grand Cube Osaka、大阪
• [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
• [Presentation] Crystallographic and NMR analyses of the novel 20S proteasome assembling chaperone PAC3 (2007)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [Presentation] In-Cell NMR Spectroscopy of Proteins inside Xenopus laevis Oocytes (2007)
  • Author(s): Tochio H., Sakai T., Tenno T., Tanaka T., Hiroaki H., Shirakawa
  • Organizer: 48th Experimental NMR conference
  • Place of Presentation: Daytona Beach, USA
• [Remarks] ホームページ等
  • URL: http://www.rinshoken.or.jp/ER/PRBP/index.html
• [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)
• [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