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Structural analysis of cell adhesion molecules that determine cell coordinate in tissue

Research Project

Project/Area Number 26440028
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionOsaka University

Principal Investigator

Suzuki Mamoru  大阪大学, たんぱく質研究所, 准教授 (40280507)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsネクチン / 構造生物学 / 結晶構造解析 / 細胞接着分子 / X線結晶構造解析
Outline of Final Research Achievements

We established recombinant expression systems for extracellular domains of mouse Nectin-1 and mouse Nectin-3 in insect cell Sf-9. First we tried to purify Nectin-1 / Nectin-3 heterodimer fraction from the mixture of cultural supernatants. However, the result of surface plasmon resonance analysis indicated the fast dissociation rate constant of heterophilic interaction between Nectin-1 and Nectin-3, suggested difficulty of stable hetero-complex purification. Thus we next established individual purification systems for Nectin-1 and Nectin-3, respectively. The purified Nectins were mixed and used for crystallization experiments. As a result, structures of Nectin-1 homodimer and Nectin-3 homodimer were obtained from mixture of purified Nectin-1 and Nectin-3 in 2.24 A and 2.58 A resolutions, respectively (PDB ID: 5B21and 5B22). Additionally, chemical crosslink experiment using BS3 crosslinker revealed that the minimal unit of Nectin-1 / Nectin-3 heterophilic complex is heterodimer.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (35 results)

All 2017 2016 2015 2014 Other

All Journal Article (18 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 18 results,  Open Access: 11 results,  Acknowledgement Compliant: 4 results) Presentation (15 results) Remarks (2 results)

  • [Journal Article] Hydroxyethyl cellulose matrix applied to serial crystallography.2017

    • Author(s)
      Michihiro Sugahara, Takanori Nakane, Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Rie Tanaka, Toru Nakatsu, Eiichi Mizohata, Fumiaki Yumoto, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata, Eriko Nango, So Iwata
    • Journal Title

      Scientific reports

      Volume: 7 Issue: 1 Pages: 703-703

    • DOI

      10.1038/s41598-017-00761-0

    • NAID

      120006223637

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.2017

    • Author(s)
      Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
    • Journal Title

      Nature

      Volume: 543 Issue: 7643 Pages: 131-135

    • DOI

      10.1038/nature21400

    • NAID

      120006344935

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Atomic resolution structure of serine protease proteinase K at ambient temperature2017

    • Author(s)
      Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Takanori Nakane, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Bunzo Mikami, Osamu Nureki, Keiji Numata, So Iwata, Michihiro Sugahara
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 45604-45604

    • DOI

      10.1038/srep45604

    • NAID

      120006027152

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent2016

    • Author(s)
      Takanori Nakane, Shinya Hanashima, Mamoru Suzuki, Haruka Saiki, Taichi Hayashi, Keisuke Kakinouchi, Shigeru Sugiyama, Satoshi Kawatake, Shigeru Matsuoka, Nobuaki Matsumori, et al
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 113 Issue: 46 Pages: 13039-13044

    • DOI

      10.1073/pnas.1602531113

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural characterization of an aldo-keto reductase (AKR2E5) from the silkworm Bombyx mori2016

    • Author(s)
      Yamamoto K., Higashiura A., Suzuki M., Shiotsuki T., Sugahara R., Fujii T., Nakagawa A.
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 474 Issue: 1 Pages: 104-110

    • DOI

      10.1016/j.bbrc.2016.04.079

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      PNAS

      Volume: 113 Issue: 11 Pages: 2828-2933

    • DOI

      10.1073/pnas.1517770113

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Oil-free hyaluronic acid matrix for serial femtosecond crystallography2016

    • Author(s)
      Michihiro Sugahara, Changyong Song, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Takanori Nakane, Fumiaki Yumoto, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata & So Iwata
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 24484-24484

    • DOI

      10.1038/srep24484

    • NAID

      120005749903

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      J. Biochem

      Volume: 未定 Issue: 5 Pages: 527-538

    • DOI

      10.1093/jb/mvv133

    • NAID

      40020833586

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.2015

    • Author(s)
      Nakane T, Song C, Suzuki M, Nango E, Kobayashi J, Masuda T, Inoue S, Mizohata E, Nakatsu T, Tanaka T, Tanaka R, Shimamura T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Iwata S, Sugahara M.
    • Journal Title

      Acta Crystallogr D Biol Crystallogr.

      Volume: 71 Issue: 12 Pages: 2519-25

    • DOI

      10.1107/s139900471501857x

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.2015

    • Author(s)
      Atsushi Kodan, Tomohiro Yamaguchi, Tomohiro Murai, Keiko Gomi, Naoki Kajiyama, Eiichi Mizohata, Mamoru Suzuki, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Jaehyun Park, Changyong Song, Takaki Hatsui, Makina Yabashi, So Iwata, Hiroaki Kato, Hideo Ago, Masaki Yamamoto & Toru Nakatsu
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 14017-14017

    • DOI

      10.1038/srep14017

    • NAID

      120005651939

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser.2015

    • Author(s)
      Tono K, Shimamura T, et al.
    • Journal Title

      J. Synchrotron Rad.

      Volume: 22 Issue: 3 Pages: 532-537

    • DOI

      10.1107/s1600577515004464

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site.2015

    • Author(s)
      Fujiwara Y, Goda N, Tamashiro T, Narita H, Satomura K, Tenno T, Nakagawa A, Oda M, Suzuki M, Sakisaka T, Takai Y, Hiroaki H.
    • Journal Title

      Protein Sci.

      Volume: 24 Issue: 3 Pages: 376-385

    • DOI

      10.1002/pro.2628

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of the replacement of aspartic acid/glutamic acid residues with asparagine/glutamine residues in RNase He1 from Hericium erinaceus on inhibition of human leukemia cell lineproliferation.2015

    • Author(s)
      Kobayashi H, Motoyoshi N, Itagaki T, Suzuki M, Inokuchi N.
    • Journal Title

      Biosci.Biotechnol.Biochem.

      Volume: 79 Issue: 2 Pages: 211-217

    • DOI

      10.1080/09168451.2014.972327

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Grease matrix as a versatile carrier of proteins for serial crystallography.2015

    • Author(s)
      Sugahara M, Shimamura T, et al.
    • Journal Title

      Nat Methods.

      Volume: 12 Issue: 1 Pages: 61-63

    • DOI

      10.1038/nmeth.3172

    • NAID

      120005682565

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Protein Structure Analyses Using X-ray Free-Electron Lasers.2014

    • Author(s)
      Mizohata E, Nango E, Sugahara M, Suzuki M, and Iwata S.
    • Journal Title

      J Cryst Soc Jap.

      Volume: 56 Pages: 241-246

    • NAID

      130004688356

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?2014

    • Author(s)
      Gallat Francois-Xavier, N. Matsugaki, P. Coussens Nathan, Yagi J. K., Boudes M., T. Higashi, Daisuke Tsuji, Tatano Yutaka, M. Suzuki, E. Mizohata, K. Tono, Y. Hatui, M. Yabashi, E. Nango, K.Itou, Coulibaly Fasseli, Tobe Stephen, Ramaswamy S., S. Iwata and Chavas M. L.
    • Journal Title

      The Royal Society

      Volume: 369 Issue: 1647 Pages: 20130497-20130497

    • DOI

      10.1098/rstb.2013.0497

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] X-Ray Crystallographic Structure of RNase Po1 That Exhibits Antitumor Activity.2014

    • Author(s)
      Hiroko Kobayashi,Takuya Katsutani, Yumiko Hara, Naomi Motoyoshi, Tadashi Itagaki, Fusamichi Akita, Akifumi Higashiura, Yusuke Yamada, Norio Inokuchi and Mamoru Suzuki
    • Journal Title

      Biol. Pharm. Bull.

      Volume: 37 Pages: 968-978

    • NAID

      130004147340

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Radically different thioredoxin domain arrangement of ERp46, an efficient disulfi de-bond introducer of the mammalian PDI family2014

    • Author(s)
      Kojima, R., Okumura, M., Masui. S., et al.
    • Journal Title

      Structure

      Volume: 22 Issue: 3 Pages: 431-443

    • DOI

      10.1016/j.str.2013.12.013

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] ヤマブシタケ由来RNaseHe1のZn複合体のX線構造解析2017

    • Author(s)
      小林弘子, 元吉尚美, 板垣正, 武部克希, 寒川剛, 鈴木守
    • Organizer
      日本薬学会第137年会
    • Place of Presentation
      宮城県仙台市仙台国際センター
    • Year and Date
      2017-03-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] M3型化膿レンサ球菌が産生する線毛タンパク質 FctA3 の結晶構造解析2016

    • Author(s)
      川剛、武部克希、中田匡宣、川端重忠、鈴木守
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      茨城県水戸市茨城県民文化センター
    • Year and Date
      2016-11-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] 高粘度結晶輸送媒体を利用したXFEL施設SACLAでの連続フェムト秒結晶構造解析2016

    • Author(s)
      菅原道泰,鈴木 守,桝田 哲哉,井上茂之,Changyong Song,中根崇智,溝端栄一,中津亨, 湯本史明, 南後恵理子, 登野健介, 沼田 圭司,岩田想
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      茨城県水戸市茨城県民文化センター
    • Year and Date
      2016-11-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] 膜蛋白質のSFXによる迅速位相決定を志向したヨウ素含有界面活性剤の開発2016

    • Author(s)
      中根崇智、花島慎弥、鈴木守、斎木悠、林太一、垣之内啓介、杉山成、川竹悟史、松岡茂、松森信明、南後恵理子、小林淳、島村達郎、木村香菜子、森千寿、国島直樹、菅原道泰、高久陽子、井上茂之、桝田哲哉、保坂俊彰、 登野健介、城地保昌、亀島敬、初井宇記、矢橋牧名、井上豪、濡木理、岩田想、村田道雄、溝端栄一
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      茨城県水戸市茨城県民文化センター
    • Year and Date
      2016-11-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] 細胞接着因子 Nectin-1/3 ヘテロ複合体の立体構造解析2016

    • Author(s)
      寒川剛、武部克希、勝谷拓也、鈴木守
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡県福岡市福岡国際会議場
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] X線自由電子レーザーを用いた新規タンパク質の立体構造決定2016

    • Author(s)
      山下恵太郎, 潘 東青, 奥田智彦, 菅原道泰, 小段篤史, 山口知宏, 村井智洋, 溝端栄一, 鈴木 守, 南後恵理子, 登野健介, 城地保昌, 亀島 敬, 初井宇記, 矢橋牧名, 岩田 想, 加藤博章, 吾郷日出夫, 山本雅貴, 中津 亨
    • Organizer
      日本薬学会第136年会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-03-26
    • Related Report
      2015 Research-status Report
  • [Presentation] ヤマブシタケ由来 RNase He1 の改変による至適 pHの変動について2016

    • Author(s)
      小林弘子, 元吉尚美, 板垣 正, 鈴木 守, 井口法男
    • Organizer
      日本薬学会第136年会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-03-26
    • Related Report
      2015 Research-status Report
  • [Presentation] fimA P. gingivalis Ⅱ型 TDC60株産生ジペプチダーゼの構造および呼吸器官への為害性2015

    • Author(s)
      菱沼光恵,田中陽子,矢口 学,桒原紀子,鈴木 守,野本たかと
    • Organizer
      日本障害者歯科学会
    • Place of Presentation
      名古屋国際会議場(愛知県名古屋市)
    • Year and Date
      2015-11-06
    • Related Report
      2015 Research-status Report
  • [Presentation] 細胞接着因子ネクチンのヘテロ複合体の結晶構造解析2015

    • Author(s)
      寒川剛、武部克希、鈴木守
    • Organizer
      日本結晶学会平成27年度年会
    • Place of Presentation
      大阪府立大学 中百舌鳥キャンパス(大阪府堺市)
    • Year and Date
      2015-10-17
    • Related Report
      2015 Research-status Report
  • [Presentation] シリアル結晶学における重原子誘導体を用いた位相決定2015

    • Author(s)
      山下恵太郎・潘東青・長谷川和也・菅原道泰・村井智洋・小段篤史・溝端栄一・鈴木 守・桝田哲哉・平田邦生・加藤博章・吾郷日出夫・熊坂 崇・山本雅貴・中津亨
    • Organizer
      日本結晶学会平成27年度年会
    • Place of Presentation
      大阪府立大学 中百舌鳥キャンパス(大阪府堺市)
    • Year and Date
      2015-10-17
    • Related Report
      2015 Research-status Report
  • [Presentation] 甘味タンパク質ソーマチンの連続フェムト秒結晶構造解析2015

    • Author(s)
      桝田 哲哉、南後 恵理子、菅原 道泰、鈴木 守、登野 健介、城地 保昌、亀島 敬、Park Jaehyun、Song Changyong、初井 宇記、矢橋 牧名、大久保 喬平、三上 文三、北畠 直文、谷 史人、岩田 想
    • Organizer
      日本農芸化学会2015年度大会
    • Place of Presentation
      岡山
    • Year and Date
      2015-03-26 – 2015-03-29
    • Related Report
      2014 Research-status Report
  • [Presentation] システイン残基改変体を用いたヤマブシタケ由来RNase He1の安定性の検討2015

    • Author(s)
      小林弘子、元吉尚美、板垣 正、鈴木 守、井口法男
    • Organizer
      日本薬学会第135年会
    • Place of Presentation
      神戸
    • Year and Date
      2015-03-25 – 2015-03-28
    • Related Report
      2014 Research-status Report
  • [Presentation] 歯周病原因菌由来HBP35の構造と機能2015

    • Author(s)
      鈴木 守、柴田恭子、 安孫子宜光
    • Organizer
      物構研サイエンスフェスタ
    • Place of Presentation
      つくば
    • Year and Date
      2015-03-17 – 2015-03-18
    • Related Report
      2014 Research-status Report
  • [Presentation] 特異的細胞接着の構造生物学的理解を目指して2014

    • Author(s)
      寒川剛・成田宏隆・勝谷拓也・中川敦史・鈴木守
    • Organizer
      日本結晶学会平成26年度年会
    • Place of Presentation
      東京
    • Year and Date
      2014-11-01 – 2014-11-03
    • Related Report
      2014 Research-status Report
  • [Presentation] アドヘレンスジャンクションで働く接着因子の立体構造と機能2014

    • Author(s)
      鈴木 守
    • Organizer
      第56回歯科基礎医学会学術大会
    • Place of Presentation
      福岡
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Remarks] 鈴木守ユニット

    • URL

      http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/index.html

    • Related Report
      2015 Research-status Report
  • [Remarks] 大阪大学蛋白質研究所 鈴木守

    • URL

      http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/

    • Related Report
      2014 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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