sbrc

KEK

論文・書籍

2017年

Experimental phase determination with selenome­thionine or mercury-derivatization in serial femtosecond crystallography.
Yamashita, K., Kuwabara, N., Nakane, T., Murai, T., Mizohata, E., Sugahara, M., Pan, D., Masuda, T., Suzuki, M., Sato, T., Kodan, A., Yamaguchi, T., Nango, E., Tanaka, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Manya, H., Endo, T., Kato, R., Senda, T., Kato, H., Iwata, S., Ago, H., Yamamoto, M., Yumoto, F. & Nakatsu, T.
IUCrJ 4, 1-9 (2017).

Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl Group-Substituted Heme Cofactor.
Kanai, Y., Harada, A., Shibata, T., Nishimura, R., Namiki, K., Watanabe, M., Nakamura, S., Yumoto, F., Senda, T., Suzuki, A., Neya, S. & Yamamoto, Y.
Biochemistry doi: 10.1021/acs.biochem.7b00457 (2017).

POMGnT1の構造解析による筋ジストロフィー疾患発症機序解明
桑原 直之, 加藤 龍一, 萬谷 博, 遠藤 玉夫
日本結晶学会誌 59, 114-120 (2017).

X-ray structure of a protease-resistant mutant form of human galectin-9 having two carbohydrate recognition domains with a metal-binding site.
Yoshida, H., Nishi, N., Wada, K., Nakamura, T., Hirashima, M., Kuwabara, N., Kato, R. & Kamitori, S.
Biochem. Biophys. Res. Commun. 490, 1287-1293 (2017).

The multidrug-resistance transporter MdfA from Escherichia coli : crystallization and X-ray diffraction analysis
Nagarathinam, K., Jaenecke, F., Nakada-Nakura, Y., Hotta, Y., Liu, K., Iwata, S., Stubbs, M.T., Nomura, N. & Tanabe, M.
Acta Cryst. F 73, 423–430 (2017).

The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6.
Harada, A., Kamimura, N., Takeuchi, K., Yu, H.Y., Masai, E. & Senda, T.
FEBS J. 284, 1855-1867 (2017).

The First Crystal Structure of a Family 129 Glycoside Hydrolase from a Probiotic Bacterium Reveals Critical Residues and Metal Co-factors.
Sato, M., Liebschner, D., Yamada, Y., Matsugaki, N., Arakawa, T., Wills, S.S., Hattie, M., Stubbs, K.A., Ito, T., Senda, T., Ashida, H. & Fushinobu, S.
J. Biol. Chem. 292, 12126-12138 (2017)

3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy.
Nagae, M., Mishra, S.K., Neyazaki, M., Oi, R., Ikeda, A., Matsugaki, N., Akashi, S., Manya, H., Mizuno, M., Yagi, H., Kato, K., Senda, T., Endo, T., Nogi, T. & Yamaguchi, Y.
Genes Cells 22, 348-359 (2017).

Crystallographic analysis of murine p24γ2 Golgi dynamics domain.
Nagae, M., Liebschner, D., Yamada, Y., Morita-Matsumoto, K., Matsugaki, N., Senda, T., Fujita, M., Kinoshita, T. & Yamaguchi, Y.
Proteins 85, 764-770 (2017).

Improved method for soluble expression and rapid purification of yeast TFIIA.
Adachi, N., Aizawa, K., Kratzer, Y., Saijo, S., Shimizu, N. & Senda ,T.
Protein Expr. Purif. 133, 50-56 (2017).


2016年

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin.
Makyio, H., Shimabukuro, J., Suzuki, T., Imamura, A., Ishida, H., Kiso, M., Ando, H. & Kato, R.
Biochem. Biophys. Res. Commun. 477, 477-482 (2016).

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.
Kuwabara, N., Manya, H., Yamada, T., Tateno, H., Kanagawa, M., Kobayashi, K., Akasaka-Manya, K., Hirose, Y., Mizuno, M., Ikeguchi, M., Toda, T., Hirabayashi, J., Senda, T., Endo, T., & Kato, R.
Proc. Natl. Acad. Sci. USA 113, 9280–9285 (2016)

Development of sample exchange robot PAM-HC for beamline BL-1A at the photon factory.
Hiraki, M., Matsugaki, N., Yamada, Y. & Senda, T.
AIP Conf. Proc. 1741, 030029 (2016).

Newly designed double surface bimorph mirror for BL-15A of the photon factory.
Igarashi, N., Nitani, H., Takeichi, Y., Niwa, Y., Abe, H., Kimura, M., Mori, T., Nagatani, Y., Kosuge, T., Kamijo, A., Koyama, A., Ohta, H. & Shimizu, N.
AIP Conf. Proc. 1741, 040021 (2016).

In-situ data collection at the photon factory macromolecular crystallography beamlines.
Yamada, Y., Hiraki, M., Matsugaki, N., Kato, R. & Senda, T.
AIP Conf. Proc. 1741, 050023 (2016).

Upgrade of small angle x-ray scattering beamline BL-6A at the photon factory.
Takagi, H., Igarashi, N., Mori, T., Saijo, S., Ohta, H., Nagatani, Y., Kosuge, T. & Shimizu, N.
AIP Conf. Proc. 1741, 030018 (2016).

Test results of a counting type SOI device for a new x-ray area detector.
Hashimoto, R., Arai, Y., Igarashi, N., Kumai, R., Miyoshi, T. & Kishimoto, S.
AIP Conf. Proc. 1741, 040031 (2016).

Software development for analysis of small-angle x-ray scattering data.
Shimizu, N., Yatabe, K., Nagatani, Y., Saijyo, S., Kosuge, T. & Igarashi,N.
AIP Conf. Proc. 1741, 050017 (2016).

On the influence of crystal size and wavelength on native SAD phasing.
Liebschner, D., Yamada, Y., Matsugaki, N., Senda, M. & Senda, T.
Acta Crystallogr. D Biol. Crystallogr. 72, 728-741 (2016).

Uncovering ancient transcription systems with a novel evolutionary indicator.
Adachi, N., Senda, T. & Horikoshi, M.
Sci. Rep. 6, 27922 (2016).

A conserved island of BAG6/Scythe is related to ubiquitin domains and participates in short hydrophobicity recognition.
Tanaka, H., Takahashi, T., Xie, Y., Minami, R., Yanagi, Y., Hayashishita, M., Suzuki, R., Yokota, N., Shimada, M., Mizushima, T., Kuwabara, N., Kato, R. & Kawahara, H.
FEBS J. 283, 662-677 (2016).

Classification and Comparison of Fucose-Binding Lectins Based on Their Structures
Makyio, H. & Kato, R.
Trends Glycosci. Glycotechnol. 28, E25–E37 (2016).

立体構造に基づいたフコースを結合するレクチンの比較と分類
牧尾 尚能, 加藤 龍一
Trends Glycosci. Glycotechnol. 28, J25–J38 (2016).

Use of multiple cryoprotectants to improve diffraction quality from protein crystals.
Senda, M., Hayashi, T., Hatakeyama, M., Takeuchi, K., Sasaki, A.T., & Senda, T.
Crystal Growth & Design. 16, 1565–1571 (2016).

A novel method of preparing the monoform structure of catalytic antibody light chain.
Hifumi, E., Matsumoto, S., Nakashima, H., Itonaga, S., Arakawa, M., Katayama, Y., Kato, R. & Uda, T.
FASEB J. 30, 895-908 (2016).

The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis.
Sumita, K., Lo, Y.H., Takeuchi, K., Senda, M., Kofuji, S., Ikeda, Y., Terakawa, J., Sasaki, M., Yoshino, H., Majd, N., Zheng, Y., Kahoud, E.R., Yokota, T., Emerling, B.M., Asara, J.M., Ishida, T., Locasale, J.W., Daikoku, T., Anastasiou, D., Senda, T. & Sasaki A.T.
Mol. Cell 61, 187-198 (2016).


2015年

Dramatic increase in SHP2 binding activity of Helicobacter pylori Western CagA by EPIYA-C duplication: its implications in gastric carcinogenesis.
Nagase, L., Hayashi, T., Senda, T. & Hatakeyama, M.
Sci. Rep. 5, 15749 (2015).

POMGNT1 is glycosylated by mucin-type O-glycans.
Xin, X., Akasaka-Manya, K., Manya, H., Furukawa, J., Kuwahara, N., Okada, K., Tsumoto, H., Higashi, N., Kato, R., Shinohara, Y., Irimura, T. & Endo, T.
Biol. Pharm. Bull. 38, 1389–1394 (2015).

Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis.
Kuwabara, N., Minami, R., Yokota, N., Matsumoto, H., Senda, T., Kawahara, H. & Kato, R.
J. Biol. Chem. 290, 9387-9398 (2015).

セレン含有糖鎖を用いた糖鎖結合タンパク質の位相決定法
牧尾尚能、加藤龍一
糖鎖の新機能開発・応用ハンドブック、津本浩平 他編 pp272-276 (2015).
エヌ・ティー・エス 2015.8.12発刊 ISBN978-4-86043-409-0

X-ray Crystallography of Sugar Related Proteins
Makyio, H. & Kato, R.
in "Glycoscience: Biology and Medicine" ed. by Taniguchi, N. et al. Springer pp175-182 (2015).


2014年

Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Sugimoto, K., Senda, M., Kasai, D., Masai, E., Fukuda, M. & Senda, T.
PLoS One 9, e92249 (2014).

Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing.
Suzuki, T., Makyio, H., Ando, H., Komura, N., Menjo, M., Yamada, Y., Imamura, A., Ishida, H., Wakatsuki, S., Kato, R. & Kiso, M.
Bioorg. Med. Chem. 22, 2090-2101 (2014).

Mechanism underlying IKK activation mediated by the linear ubiquitin chain assembly complex (LUBAC).
Fujita, H., Rahighi, S., Akita, M., Kato, R., Sasaki, Y., Wakatsuki, S. & Iwai, K.
Mol. Cell. Biol. 34, 1322-1335 (2014).

Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism.
Suzuki, H., Tabata, K., Morita, E., Kawasaki, M., Kato, R., Dobson, R.C., Yoshimori, T. & Wakatsuki, S.
Structure 22, 47-58 (2014).

A New Structure Determination Method of Lectins, Using a Selenium-containing Sugar Ligand.
Makyio, H. & Kato, R.
in "Lectins / Methods in Molecular Biology 1200" ed. by J. Hirabayashi et al. Humana Press pp491-499 (2014).


2013年

Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity.
Kuwabara, N., Hu, D., Tateno, H., Makyio, H., Hirabayashi, J. & Kato, R.
FEBS Lett. 587, 3620-3625 (2013).

Improvement of an Automated Protein Crystal Exchange System PAM for High-throughput Data Collection.
Hiraki, M., Yamada, Y., Chavas, L.M., Wakatsuki, S. & Matsugaki, N.
J. Synchrotron Radiat. 20, 890-893 (2013).

Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A.
Yamada, Y., Chavas, L.M., Igarashi, N., Hiraki, M., Wakatsuki, S. & Matsugaki, N.
J. Synchrotron Radiat. 20, 938-942 (2013).

New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography.
Chavas, L.M., Nagae, T., Yamada, H., Watanabe, N., Yamada, Y., Hiraki, M. & Matsugaki, N.
J. Synchrotron Radiat. 20, 838-842 (2013).

Structural basis for phosphorylation-triggered autophagic clearance of Salmonella.
Rogov, V.V., Suzuki, H., Fiskin, E., Wild, P., Kniss, A., Rozenknop, A., Kato, R., Kawasaki, M., McEwan, D.G., Löhr, F., Güntert, P., Dikic, I., Wakatsuki, S. & Dötsch, V.
Biochem. J. 454, 459-466 (2013).

Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6.
Makyio, H., Takeuchi, T., Tamura, M., Nishiyama, K., Takahashi, H., Natsugari, H., Arata, Y., Kasai, K., Yamada, Y., Wakatsuki, S. & Kato, R.
Glycobiology 23, 797-805 (2013).

Direct metal recognition by guanine nucleotide exchange factor in the initial step of exchange reaction.
Uejima, T., Ihara, K., Sunada, M., Kawasaki, M., Ueda, T., Kato, R., Nakano, A. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 69, 345-351 (2013).

Data Management System at the Photon Factory Macromolecular Crystallography Beamline
Yamada, Y., Matsugaki, N., Chavas, L.M., Hiraki, M., Igarashi, N. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425, 012017 (2013).

Current status and future prospects of an automated sample exchange system PAM for protein crystallography
Hiraki, M., Yamada, Y., Chavas, L.M., Matsugaki, N., Igarashi, N. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425, 012014 (2013).

10 years of protein crystallography at AR-NW12A beamline
Chavas, L.M., Matsugaki, N., Yamada, Y., Hiraki, M., Igarashi, N., Suzuki, M. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425 012008 (2013).



2012年

Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs(BAR) domain of Arfaptin-2 determined by Arl1 GTPase.
Nakamura, K., Man, Z., Xie, Y., Hanai, A., Makyio, H., Kawasaki, M., Kato, R., Shin, H.W., Nakayama, K. & Wakatsuki, S.
J. Biol. Chem. 287, 25478-25489 (2012).

Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory
Chavas, L.M., Matsugaki, N., Yamada, Y., Hiraki, M., Igarashi, N., Suzuki, M. & Wakatsuki S.
J. Synchrotron Radiat. 19, 450-454 (2012).

S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS
Ru, H., Zhao, L., Ding, W., Jiao, L., Shaw, N., Liang, W., Zhang, L., Hung, L, Matsugaki, N., Wakatsuki, S. & Liu, Z.
Acta Crystallogr. D Biol. Crystallogr. 68, 521-530 (2012).

Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis
Makyio, H., Ohgi, M., Takei, T., Takahashi, S., Takatsu, H., Katoh, Y., Hanai, A., Ueda, T., Kanaho, Y., Xie, Y., Shin, H.W., Kamikubo, H., Kataoka, M., Kawasaki, M., Kato, R., Wakatsuki, S. & Nakayama, K.
EMBO J. 31, 2590-2603 (2012).

High-pressure-induced water penetration into 3-isopropylmalage dehydrogenase
Nagae, T., Kawamura, T., Chavas, L.M.G., Niwa, K., Hasegawa, M., Kato, C. & Watanabe, N.
Acta Crystallogr. D Biol. Crystallogr. 68, 300-309 (2012).

Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2
Okazaki, S., Kato, R., Uchida, Y., Taguchi, T., Arai, H. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 68, 117-123 (2012).

Structure of a compact conformation of linear diubiquitin Rohaim, A., Kawasaki, M., Kato, R., Dikic, I. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 68, 102-108 (2012).

PF構造生物学ビームラインにおける全自動回折データセット収集/処理システムの開発
山田悠介、平木雅彦、松垣直宏、Leonard M. G. Chavas、五十嵐教之、若槻壮市
日本結晶学会誌 Vol. 54, No.6 359-363 (2012).

ヒト由来Evectin-2のリン脂質結合特異性についての構造学的洞察
岡崎誠司、加藤龍一、若槻壮市、内田安則、田口友彦、新井洋由
日本結晶学会誌 Vol. 54, No.2 101-106 (2012).



2011年

Intracellular phosphatidylserine is essential for retrograde membrane traffic through endosomes
Uchida, Y., Hasegawa, J., Chinnapen, D., Inoue, T., Okazaki, S., Kato, R., Wakatsuki, S., Misaki, R., Koike, M., Uchiyama, Y., Iemura, S., Natsume, T., Kuwahara, R., Nakagawa, T., Nishikawa, K., Mukai, K., Miyoshi, E., Taniguchi, N., Sheff, D., Lencer, W.I., Taguchi, T. & Arai, H.
Proc. Natl. Acad. Sci. USA 108, 15846-15851 (2011).

UV LED lighting for automated crystal centring
Chavas, L.M., Yamada, Y., Hiraki, M., Igarashi, N., Matsugaki, N. & Wakatsuki, S.
J. Synchrotron Radiat. 18, 11-15 (2011).

Improved Inactivation Effect of Bacteria: Fabrication of Mesoporous Anatase Films with Fine Ag Nanoparticles Prepared by Coaxial Vacuum Arc Deposition
Oveisi, H., Rahighi, S., Jiang, X., Agawa, Y., Beitollahi, A., Wakatsuki, S. & Yamauchi, Y.
Chem. Lett. 40, 420-422 (2011).

Selective binding of linear ubiquitin chains to NEMO in NF-kB activation
Ikeda, F., Rahighi, S., Wakatsuki, S. & Dikic, I.
Adv. Exp. Med. Biol. 691, 107-114 (2011).


2010年

GDP-bound and nucleotide-free intermediates of the guanine nucleotideexchange in the Rab5/Vps9 system
Uejima, T., Ihara, K., Goh, T., Ito, E., Sunada, M., Ueda, T., Nakano, A. & Wakatsuki, S.
J. Biol. Chem. 285, 36689-36697 (2010).

Crystallization of small proteins assisted by green fluorescent protein
Suzuki, N., Hiraki, M., Yamada, Y., Matsugaki, N., Igarashi, N., Kato, R., Dikic, I., Drew, D., Iwata, S., Wakatsuki, S. & Kawasaki, M.
Acta Crystallogr. D Biol. Crystallogr. 66, 1059-1066 (2010).

Crystal structure of cyclic Lys48-linked tetraubiquitin
Satoh, T., Sakata, E., Yamamoto, S., Yamaguchi, Y., Sumiyoshi, A., Wakatsuki, S. & Kato, K.
Biochem. Biophys. Res. Commun. 400, 329-333 (2010).

Unusual antibacterial property of mesoporous titania films: drastic improvement by controlling surface area and crystallinity
Oveisi, H., Rahighi, S., Jiang, X., Nemoto, Y., Beitollahi, A., Wakatsuki, S. & Yamauchi, Y.
Chem. Asian J. 5, 1978-1983 (2010).

Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2DeltaGF122) and structural roles of F122 intarget recognition
Inuzuka, T., Suzuki, H., Kawasaki, M., Shibata, H., Wakatsuki, S. & Maki, M.
BMC Struct. Biol. 10, 25 (2010).

GMF is an evolutionarily developed ADF/cofilin-super family protein involved in the Arp2/3 complex-mediated organization of the actin cytoskeleton
Nakano, K., Kuwayama, H., Kawasaki, M., Numata, O. & Takaine, M.
Cytoskeleton 67, 373-382 (2010).

Complexity in influenza virus targeted drug design: interaction with human sialidases
Chavas, L.M., Kato, R., Suzuki, N., von Itzstein, M., Mann, M.C., Thomson, R.J., Dyason, J.C., McKimm-Breschkin, J., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E. & Wakatsuki, S.
J. Med. Chem. 53, 2998-3002 (2010).

Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer
Kudo, N., Kumagai, K., Matsubara, R., Kobayashi, S., Hanada, K., Wakatsuki, S. & Kato, R.
J. Mol. Biol. 396, 245-251 (2010).

Crystal Structure of UbcH5b-Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2-Ub Conjugates
Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Tanaka, K., Wakatsuki, S. & Kato, K.
Structure 18, 138-147 (2010).

「-リボソーム構造解析の先駆者- アダ・ヨナット教授に聞く」
聞き手:若槻壮市  現代化学 2010年10月号 No.475 2010.9.18発刊 0348710

ターゲットタンパク研究プログラムで目指すX線構造解析の高度化:フォトンファクトリーにおける技術開発
若槻壮市、山田悠介、Leonard M.G. Chavas、五十嵐教之、川崎政人、加藤龍一、平木雅彦、松垣直宏
薬学雑誌 Vol.130, No.5 631-640 (2010).

ターゲットタンパク研究プログラムの目指す放射光構造生物学
平田邦生, 山本雅貴, 松垣直宏, 若槻壮市
日本結晶学会誌 Vol. 52, No.1 43-47 (2010).

「入門 構造生物学 -放射光X線と中性子で最新の生命現象を読み解く-」
加藤龍一、山田悠介、平木雅彦、松垣直宏、五十嵐教之、川崎政人 他著
高エネルギー加速器研究機構 構造生物学研究センター 編 加藤龍一 編集
共立出版 2010.4.25発刊 ISBN978-4-320-05704-3


2009年

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory
Yamada, Y., Hiraki, M., Sasajima, K., Matsugaki, N., Igarashi, N., Amano, Y., Warizaya, M., Sakashita, H., Kikuchi, T., Mori, T., Toyoshima, A., Kishimoto, S. & Wakatsuki, S.
AIP Conf. Proc. 1234, 415-418 (2009).

Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes
Hiraki, M., Watanabe, S., Chavas, L.M.G., Yamada, Y., Matsugaki, N., Igarashi, N., Wakatsuki, S., Fujihashi, M., Miki, K., Baba, S., Ueno, G., Yamamoto, M., Suzuki, M., Nakagawa, A., Watanabe, N. & Tanaka, I.
AIP Conf. Proc. 1234, 673-676 (2009).

Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S. & Dikic, I.
Cell 136, 1098-1109 (2009).

Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain
Nagae, M., Nishi, N., Murata, T., Usui, T., Nakamura, T., Wakatsuki, S. & Kato, R.
Glycobiology 19, 112-117 (2009).

高難度蛋白質をターゲットとした放射光X線結晶構造解析技術の開発
若槻壮市、山本雅貴、田中勲、三木邦夫、中川敦史 他著
長野哲雄、若槻壮市、高木淳一、古谷利夫 編
「融合発展する構造生物学とケミカルバイオロジーの最前線」共立出版 (2009).

NEMOによる直鎖状ユビキチン鎖の特異的認識はNF-κB活性化に重要である
池田史代、Simin Rahighi、若槻壮市、川崎政人
実験医学 Vol.27, No.14, 2240-2243 (2009).

エフェクタータンパク質群によるRab27取り込みへの構造的知見
レオナルド シャバス、伊原健太郎、川崎政人、若槻壮市
日本結晶学会誌 Vol. 51, No.6 334-339 (2009).

The mechanism of Ca2+-dependent recognition of Alix by ALG-2: insights from X-ray crystal structures
Suzuki H, Kawasaki M, Inuzuka T, Okumura M, Kakiuchi T, Shibata H, Wakatsuki S, Maki M
Biochem. Soc. Trans. 37, 190-194 (2009).


2008年

Nucleotide-Dependent Conformational Changes and Assembly of the AAA ATPase SKD1/VPS4B
Inoue, M., Kamikubo, H., Kataoka, M., Kato, R., Yoshimori, T., Wakatsuki, S. & Kawasaki, M.
Traffic 9, 2180-2189 (2008).

Crystallization and X-ray diffraction analysis of N-terminally truncated human ALG-2
Suzuki, H., Kawasaki, M., Kakiuchi, T., Shibata, H., Wakatsuki, S. & Maki, M.
Acta Crystallogr. F Struct. Biol. Commun. 64, 974-977 (2008).

1,2-alpha-l-Fucosynthase: A glycosynthase derived from an inverting alpha-glycosidase with an unusual reaction mechanism
Wada, J., Honda, Y., Nagae, M., Kato, R., Wakatsuki, S., Katayama, T., Taniguchi, H., Kumagai, H., Kitaoka, M. & Yamamoto, K.
FEBS Lett. 582, 3739-3743 (2008).

Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism
Suzuki, H., Kawasaki, M., Inuzuka, T., Okumura, M., Kakiuchi, T., Shibata, H., Wakatsuki, S. & Maki, M.
Structure 16, 1562-1573 (2008).

Elucidation of Rab27 Recruitment by Its Effectors: Structure of Rab27a Bound to Exophilin4/Slp2-a
Chavas, L.M.G., Ihara, K., Kawasaki, M., Torii, S., Uejima, T., Kato, R., Izumi, T. & Wakatsuki, S.
Structure 16, 1468-1477 (2008).

Purification, crystallization and preliminary X-ray crystallographic analysis of Rab27a GTPase in complex with exophilin4/Slp2-a effector
Chavas L.M., Ihara, K., Kawasaki, M., Kato, R., Izumi, T. & Wakatsuki, S.
Acta Crystallogr. F Struct. Biol. Commun. 64, 599-601 (2008).

Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T
Murakami, K., Stewart, M., Nozawa, K., Tomii, K., Kudou, N., Igarashi, N., Shirakihara, Y., Wakatsuki, S., Yasunaga, T. & Wakabayashi, T.
Proc. Natl. Acad. Sci. USA 105, 7200-7205 (2008).

Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: implications for asymmetric cell division in Drosophila
Yousef, M.S., Kamikubo, H., Kataoka, M., Kato, R. & Wakatsuki, S.
Protein Sci. 17, 908-917 (2008).

Development of an X-ray HARP-FEA detector system for high-throughput protein crystallography
Miyoshi, T., Igarashi, N., Matsugaki, N., Yamada, Y., Hirano, K., Hyodo, K., Tanioka, K., Egami, N., Namba, M., Kubota, M., Kawai, T. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 281-284 (2008).

X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory
Igarashi, N., Ikuta, K., Miyoshi, T., Matsugaki, N., Yamada, Y., Yousef, M.S. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 292-295 (2008).

Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines
Yamada, Y., Honda, N., Matsugaki, N., Igarashi, N., Hiraki, M. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 296-299 (2008).

High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines
Hiraki, M., Watanabe, S., Honda, N., Yamada, Y., Matsugaki, N., Igarashi, N., Gaponov, Y. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 300-303 (2008).

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide
Kudo, N., Kumagai, K., Tomishige, N., Yamaji, T., Wakatsuki, S., Nishijima, M., Hanada, K. & Kato, R.
Proc. Natl. Acad. Sci. USA 105, 488-493 (2008).

Structural Analysis of the Human Galectin-9 N-terminal Carbohydrate Recognition Domain Reveals Unexpected Properties that Differ from the Mouse Orthologue
Nagae, M., Nishi, N., Nakamura-Tsuruta, S., Hirabayashi, J., Wakatsuki, S. & Kato, R.
J. Mol. Biol. 375, 119-135 (2008).

Biophysical methods: structure, function and dynamics studies of macromolecular assemblies using electrons, lasers, neutrons and X-rays
Hasnain, S.S. & Wakatsuki, S.
Curr. Opin. Struct. Biol. 18, 577-580 (2008).

蛋白質X線結晶構造解析ー放射光を利用した回折実験
五十嵐教之
蛋白質科学会アーカイブ, 200

糖鎖情報の独自性と普遍性「糖鎖-ガレクチン蛋白質間の相互作用の分子機構」
加藤龍一、長江雅倫、若槻壮市
蛋白質核酸酵素 Vol. 53 No. 12 1670-1675 (2008).

特集タンパク3000プロジェクトの産んだもの、第Ⅰ部、成果とインパクト:個別的解析拠点の研究成果、「翻訳後修飾と輸送、真核生物における構造機能生物学」
若槻壮市・加藤龍一・川崎政人・五十嵐教之・平木雅彦
蛋白質核酸酵素 Vol. 53 No. 5 628-631 (2008).

ビフィズス菌由来AfcAフコシダーゼ触媒ドメインの立体構造解析
長江雅倫、土屋敦子、山本憲二、片山高嶺、若槻壮市、加藤龍一
日本結晶学会誌 Vol. 50, No.2 138-143 (2008).


2007年

Design and Construction of the High-speed Network Connecting All the Protein Crystallography Beam Lines at the Photon Factory
Matsugaki, N., Yamada, Y., Igarashi, N. & Wakatsuki, S.
AIP Conf. Proc. 879, 1936-1939 (2007).

Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory
Hiraki, M., Watanabe, S., Yamada, Y., Matsugaki, N., Igarashi, N., Gaponov, Y. & Wakatsuki, S.
AIP Conf. Proc. 879, 1924-1927 (2007).

Development of Control Applications for High-Throughput Protein Crystallography Experiments
Gaponov, Y.A., Matsugaki, N., Honda, N., Sasajima, K., Igarashi, N., Hiraki, M., Yamada, Y. & Wakatsuki, S.
AIP Conf. Proc. 879, 1932-1935 (2007).

BL-17A, A New Protein Micro-Crystallography Beam Line of the Photon Factory
Igarashi, N., Matsugaki, N., Yamada, Y., Hiraki, M., Koyama, A., Hirano, K., Miyoshi, T. & Wakatsuki, S.
AIP Conf. Proc., 879, 812-815 (2007).

Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Das, M., Kobayashi, M., Yamada, Y., Sreeramulu, S., Ramakrishnan, C., Wakatsuki, S., Kato, R. & Varadarajan, R.
J. Mol. Biol. 372, 1278-1292 (2007).

Structural Basis for Recognition of High Mannose Type Glycoproteins by Mammalian Transport Lectin VIP36
Satoh, T., Cowieson, N.P., Hakamata, W., Ideo, H., Fukushima, K., Kurihara, M., Kato, R., Yamashita, K. & Wakatsuki, S.
J. Biol. Chem. 282, 28246-28255 (2007).

Structure of the small GTPase Rab27b shows an unexpected swapped dimer
Chavas, L.M., Torii, S., Kamikubo, H., Kawasaki, M., Ihara, K., Kato, R., Kataoka, M., Izumi, T. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 63, 769-779 (2007).

Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Inoue, M., Shiba, T., Ihara, K., Yamada, Y., Hirano, S., Kamikubo, H., Kataoka, M., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Traffic 8, 904-913 (2007).

Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
Nagae, M., Tsuchiya, A., Katayama, T., Yamamoto, K., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 282, 18497-18509 (2007).

X-ray phase imaging of biological soft tissue using a direct-sensing x-ray HARP tube camera
Hirano, K., Miyoshi, T., Igarashi, N., Takeda, T., Wu, J., Lwin, T.T., Kubota, M., Egami, N., Tanioka, K., Kawai, T. & Wakatsuki, S.
Phys. Med. Biol. 52, 2545-2552 (2007).

フォトンファクトリー構造生物ビームラインにおける自動化に向けた取り組み
五十嵐教之, 平木雅彦, 松垣直宏, 山田悠介, 若槻壮市
日本結晶学会誌 Vol. 49, No.6 359-363 (2007).

FIP3による低分子量GTPase Rab11の認識機構の研究
志波智生、古賀裕士、申 惠媛、中山和久、川崎政人、加藤龍一、若槻壮市
日本結晶学会誌 Vol. 49, No.4 231-237 (2007).

小特集 結晶評価技術の新展開、解説、「蛋白質結晶評価技術の新展開」
平木雅彦、五十嵐教之、加藤龍一、山田悠介、松垣直宏、川崎政人、若槻壮市
日本結晶成長学会誌 Vol. 34 No. 3 131-138 (2007).


2006年

Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain
Hirano, S., Suzuki, N., Slagsvold, T., Kawasaki, M., Trambaiolo, D., Kato, R., Stenmark, H. & Wakatsuki, S.
Nat. Struct. Mol. Biol. 13, 1031-1032 (2006).

Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability
Yogosawa, S., Kawasaki, M., Wakatsuki, S., Kominami, E., Shiba, Y., Nakayama, K., Kohsaka, S. & Akazawa, C.
Biochem. Biophys. Res. Commun. 350, 82-90 (2006).

Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition
Nagae, M., Nishi, N., Murata, T., Usui, T., Nakamura, T., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 281, 35884-35893 (2006).

Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope
Shiba, T., Kakuda, S., Ishiguro, M., Morita, I., Oka, S., Kawasaki, T., Wakatsuki, S. & Kato, R.
Proteins 65, 499-508 (2006).

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1
Shiba, T., Koga, H., Shin, H.W., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Proc. Natl. Acad. Sci. USA 103, 15416-15421 (2006).

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses
Hiraki, M., Kato, R., Nagai, M., Satoh, T., Hirano, S., Ihara, K., Kudo, N., Nagae, M., Kobayashi, M., Inoue, M., Uejima, T., Oda, S., Chavas, L.M., Akutsu, M., Yamada, Y., Kawasaki, M., Matsugaki, N., Igarashi, N., Suzuki, M. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 62, 1058-165 (2006).

Structural Basis of Carbohydrate Transfer Activity by Human UDP-GalNAc: Polypeptide alpha-N-Acetylgalactosaminyltransferase (pp-GalNAc-T10)
Kubota, T., Shiba, T., Sugioka, S., Furukawa, S., Sawaki, H., Kato, R., Wakatsuki, S. & Narimatsu, H.
J. Mol. Biol. 359, 708-727 (2006).

Structures of carbohydrate recognition domain of Ca2+ -independent cargo receptors Emp46p and Emp47p
Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Yamada, Y., Igarashi, N., Kato, R., Nakano, A. & Wakatsuki, S.
J. Biol. Chem. 281, 10410-10419 (2006).

Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting
Hirano, S., Kawasaki, M., Ura, H., Kato, R., Raiborg, C., Stenmark, H. & Wakatsuki, S.
Nat. Struct. Mol. Biol. 13, 272-277 (2006).


2005年

Structural basis for transcription inhibition by tagetitoxin
Vassylyev, D.G., Svetlov, V., Vassylyeva, M.N., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S. & Artsimovitch, I.
Nat. Struct. Mol. Biol. 12, 1086-1093 (2005).

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain
Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K. & Wakatsuki, S.
FEBS Lett. 579, 5385-5391.

Structural basis of transcription inhibition by antibiotic streptolydigin
Temiakov, D., Zenkin, N., Vassylyeva, M.N., Perederina, A., Tahirov, T.H., Kashkina, E., Savkina, M., Zorov, S., Nikiforov, V., Igarashi, N., Matsugaki, N., Wakatsuki, S., Severinov, K. & Vassylyev, D.G.
Mol. Cell. 19, 655-666 (2005).

Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins
Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H. & Vassylyev, D.G.
Cell 122, 351-363 (2005).

Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition
Chang, C.I., Ihara, K., Chelliah, Y., Mengin-Lecreulx, D., Wakatsuki, S. & Deisenhofer, J.
Proc. Natl. Acad. Sci. USA 102, 10279-10284 (2005).

Molecular mechanism of ubiquitin recognition by GGA3 GAT domain
Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K. & Wakatsuki, S.
Genes Cells 10, 639-654 (2005).

Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic
Yamada, Y., Inoue, M., Shiba, T., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 61, 731-736 (2005).

Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain
Slagsvold, T., Aasland, R., Hirano, S., Bache, K.G., Raiborg, C., Trambaiolo, D., Wakatsuki, S. & Stenmark, H.
J. Biol. Chem. 280, 19600-19606 (2005).

Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition
Chavas, L.M., Tringali, C., Fusi, P., Venerando, B., Tettamanti, G., Kato, R., Monti, E. & Wakatsuki, S.
J. Biol. Chem. 280, 469-475 (2005).

Membrane recruitment of effector proteins by Arf and Rab GTPases
Kawasaki, M., Nakayama, K. & Wakatsuki, S.
Curr. Opin. Struct. Biol. 15, 681-689 (2005).

入門講座、こんなことができる放射光(10)、「構造プロテオミクス科学時代の放射光結晶学」
若槻壮市
日本結晶学会誌 Vol. 47, No.6 380-389 (2005).

総説、「GGA-メンブレン・トラフィックを調節する新規のクラスリンアダプターの構想と機能-」
中山和久、若槻壮市
生化学 第77巻 第11号 1367-1381 (2005).

みにれびゅう、「HNK-1糖鎖の生合成に必須な糖転移酵素GlcAT-Pのユニークな糖鎖基質認識機構」
志波智生、角田品子、岡昌吾、石黒正路、川嵜敏祐、若槻壮市、加藤龍一
生化学 第77巻 第2号 153-158 (2005).

特集構造ゲノムプロジェクトの進展、「蛋白質X線結晶構造解析手法の成熟」
若槻壮市、加藤龍一、五十嵐教之、川崎政人、松垣直宏、平木雅彦、山田悠介
蛋白質核酸酵素 Vol. 50 No. 7 846-852 (2005).


2004年

Insights into the phosphoregulation of beta-secretase sorting signal by the VHS domain of GGA1
Shiba, T., Kametaka, S., Kawasaki, M., Shibata, M., Waguri, S., Uchiyama, Y. & Wakatsuki, S.
Traffic 5, 437-448 (2004).

Structural basis for acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1
Kakuda, S., Shiba, T., Ishiguro, M., Tagawa, H., Oka, S., Kajihara, Y., Kawasaki, T., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 279, 22693-22703 (2004).

GAT (GGA and Tom1) domain responsible for ubiquitin binding and ubiquitination
Shiba, Y., Katoh, Y., Shiba, T., Yoshino, K., Takatsu, H., Kobayashi, H., Shin, H.W., Wakatsuki, S. & Nakayama, K.
J. Biol. Chem. 279, 7105-7111 (2004).

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments
Gaponov, Y., Igarashi, N., Hiraki, M., Sasajima, K., Matsugaki, N., Suzuki, M., Kosuge, T. & Wakatsuki, S.
J. Synchrotron Radiat. 11, 17-20 (2004).

ゲノミクス・プロテオミクスの新展開 生物情報の解析と応用 「X線結晶構造解析 タンパク質結晶X線回折実験における自動化」
若槻壮市、平木雅彦、Yurii Gaponov、松垣直宏、五十嵐教之、鈴木守
第2編 618-622、NTS inc. 今中忠行京都大学大学院工学研究科教授監修、2004.4.5発刊。ISBN4-86043-049-2

ゲノミクス・プロテオミクスの新展開 生物情報の解析と応用 「X線結晶構造解析 タンパク質結晶構造解析ビームライン(Photon Factory)」
鈴木守、五十嵐教之、松垣直宏、若槻壮市
第2編 612-617、NTS inc. 今中忠行京都大学大学院工学研究科教授監修、2004.4.5発刊。ISBN4-86043-049-2

「タンパク質の成熟:糖鎖修飾と輸送」
若槻壮市
2004第18回「大学と科学」公開シンポジウム講演収録集 タンパク質のかたちから生命のなぞを解く。生物マシーナリー構造生物学の最前線, 51-65 (2004).


2003年

Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Nat. Struct. Biol. 10, 386-393 (2003).

The structure and function of GGAs, the traffic controllers at the TGN sorting crossroads
Nakayama, K. & Wakatsuki, S.
Cell Struct. Funct. 28, 431-442 (2003).


2002年

Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain
Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K. & Wakatsuki, S.
Nat. Struct. Biol. 9, 527-531 (2002).

Structural basis for recognition of acidic-cluster dileucine sequence by GGA1
Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K. & Wakatsuki, S.
Nature 415, 937-941 (2002).

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