Structural study of a huge respiratory supermolecule hemocyanin

• Project/Area Number: 26291008
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Hokkaido University
• Principal Investigator: Tanaka Yoshikazu 北海道大学, 先端生命科学研究科(研究院), 准教授 (20374225)
• Co-Investigator(Kenkyū-buntansha): 姚 閔 北海道大学, 先端生命科学研究科(研究院), 教授 (40311518) ; 加藤 公児 北海道大学, 先端生命科学研究科(研究院), 助教 (30452428)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000); Fiscal Year 2016: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2015: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2014: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
• Keywords: X線結晶構造解析 / ヘモシアニン / 巨大蛋白質会合体 / 酸素運搬 / 糖鎖 / タンパク質 / 構造解析 / 蛋白質 / X線結晶解析 / 軟体動物 / 巨大分子

Outline of Final Research Achievements

In this study, we have determined the X-ray crystal structure of intact hemocyanin from Japanese flying squid at 3.0 angstrom resolution. The structure urevealed the architecture of hemocyanin composed of a cylindrical wall region and five collar regions, in which the dimers of functional units (FUs) hierarchically associated to form the entire decamer. Furthermore, the roles of carbohydrates in assembly, and conserved sulfur-containing residues in copper incorporation, were revealed.

Research Products

• [Int'l Joint Research] マックスプランク研究所(ドイツ)
• [Int'l Joint Research] Max Planck Institute(ドイツ)
• [Journal Article] Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by the iron-sulfur protein TtuA (2017)
  • Author(s): Minghao Chen, Shin-ichi Asai, Shun Narai, Shusuke Nambu, Naoki Omura, Yuriko Sakaguchi, Tsutomu Suzuki, Masao Ikeda-Saito, Kimitsuna Watanabe, Min Yao, Naoki Shigi and, Yoshikazu Tanaka
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 印刷中
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural properties of phycoerythrin from dulse palmaria palmata (2017)
  • Author(s): Yoshikatsu Miyabe, Tomoe Furuta, Tomoyuki Takeda, Gaku Kanno, Takeshi Shimizu, Yoshikazu Tanaka, Zuoqi Gai, Hajime Yasui, Hideki Kishimura
  • Journal Title: Journal of Food Biology Volume: 41 Issue: 1 Pages: e12301-e12301
  • DOI: 10.1111/jfbc.12301
  • NAID: 120006382291
  • Peer Reviewed / Open Access
• [Journal Article] Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38 (2016)
  • Author(s): 179.K. Oshima, Y. Kakiuchi, Y. Tanaka, T. Ueda, T. Nakashima, M. Kimura, and M. Yao
  • Journal Title: Biochem. Biophys. Res. Commun Volume: ４７４ Issue: 3 Pages: 541-546
  • DOI: 10.1016/j.bbrc.2016.04.118
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus (2016)
  • Author(s): Chen M, Narai S, Omura N, Shigi N, Chimnaronk S, Tanaka Y, Yao M
  • Journal Title: Acta Crystallographica Section F Structural Biology Communications Volume: F72 Issue: 10 Pages: 777-781
  • DOI: 10.1107/s2053230x16014242
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] 超巨大蛋白質会合体ヘモシアニンのX線結晶構造解析 (2016)
  • Author(s): 松野明日香，田中良和
  • Journal Title: 日本結晶学会誌 Volume: 58 Pages: 91-95
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin. (2015)
  • Author(s): Asuka Matsuno; Zuoqi Gai; Miyuki Tanaka; Koji Kato; Sanae Kato; Tsuyoshi Katoh; Takeshi Shimizu; Takeya Yoshioka; Hideki Kishimura; Yoshikazu Tanaka; Min Yao.
  • Journal Title: Journal of Structural Biology Volume: 190 Issue: 3 Pages: 379-382
  • DOI: 10.1016/j.jsb.2015.04.015
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution (2015)
  • Author(s): Zuoqi Gai, Asuka Matsuno, Koji Kato, Sanae Kato, Md Rafiqul Islam Khan, Takeshi Shimizu, Takeya Yoshioka, Yuki Kato, Hideki Kishimura, Gaku Kanno, Yoshikatsu Miyabe, Tohru Terada Yoshikazu Tanaka, and Min Yao
  • Journal Title: Structure Volume: 23 Issue: 12 Pages: 2204-2212
  • DOI: 10.1016/j.str.2015.09.008
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural basis for pore-forming mechanism of staphylococcal α-hemolysin (2015)
  • Author(s): Takaki Sugawara, Daichi Yamashita, Koji Kato, Zhao Peng, Junki Ueda, Jun Kaneko, Yoshiyuki Kamio, Yoshikazu Tanaka, Min Yao
  • Journal Title: Toxicon Volume: 108 Pages: 226-231
  • DOI: 10.1016/j.toxicon.2015.09.033
  • NAID: 120005898548
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18S rRNA (2014)
  • Author(s): Satoshi Ito, Sayuri Horikawa, Tateki Suzuki, Hiroki Kawauchi, Yoshikazu Tanaka, Takeo Suzuki, and Tsutomu Suzuki
  • Journal Title: The Journal of Biological Chemistry Volume: 289 Issue: 52 Pages: 35724-35730
  • DOI: 10.1074/jbc.c114.602698
  • Peer Reviewed / Open Access
• [Journal Article] Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins (2014)
  • Author(s): Daichi Yamashita, Takaki Sugawara, Miyu Takeshita, Jun Kaneko, Yoshiyuki Kamio, Isao Tanaka, Yoshikazu Tanaka, and Min Yao
  • Journal Title: Nature Communications Volume: 5 Issue: 1 Pages: 4897-4897
  • DOI: 10.1038/ncomms5897
  • NAID: 120005572422
  • Peer Reviewed / Open Access
• [Journal Article] Structural and genomic DNA analysis of the putative TetR transcriptional repressor SCO7518 from Streptomyces coelicolor A3(2) (2014)
  • Author(s): Takeshi Hayashi, Yoshikazu Tanaka, Naoki Sakai, Ui Okada, Min Yao, Nobuhisa Watanabe, Tomohiro Tamura, and Isao Tanaka
  • Journal Title: FEBS Letters Volume: 588 Issue: 23 Pages: 4311-4318
  • DOI: 10.1016/j.febslet.2014.09.037
  • Peer Reviewed / Open Access
• [Journal Article] Anchoring protein crystals to mounting loops with hydrogel using inkjet technology (2014)
  • Author(s): Akira Shinoda, Yoshikazu Tanaka, Min Yao and Isao Tanaka
  • Journal Title: Acta Crystallographica Section D Volume: D70 Issue: 11 Pages: 2794-2799
  • DOI: 10.1107/s139900471401476x
  • NAID: 120005530838
  • Peer Reviewed
• [Journal Article] Nucleoid compaction by MrgAAsp56Ala/Glu60Ala does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophage (2014)
  • Author(s): Yuri Ushijima, Ryosuke L. Ohniwa, Atsushi Maruyama, Shinji Saito, Yoshikazu Tanaka, and Kazuya Morikawa
  • Journal Title: FEMS Microbiology Letters Volume: 360 Issue: 2 Pages: 144-151
  • DOI: 10.1111/1574-6968.12598
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of a bacterial Asn-transamidosome (2014)
  • Author(s): Tateki Suzuki, Keitaro Yamashita, Yoshikazu Tanaka, Isao Tanaka, and Min Yao
  • Journal Title: Acta Crystallographica Section F Volume: F70 Issue: 6 Pages: 790-793
  • DOI: 10.1107/s2053230x14007274
  • Peer Reviewed
• [Presentation] リジニバチルス菌由来毒素タンパク質Bin toxinの構造解析 (2017)
  • Author(s): 松本勇，加藤公児，Panadda Boonserm，田中良和，姚閔
  • Organizer: 2016年度量子ビームサイエンスフェスタ・第8回MLFシンポジウム・第34回PFシンポジウム
  • Place of Presentation: つくば国際会議場（茨城県，つくば市）
  • Year and Date: 2017-03-14
• [Presentation] Encapsulation of Biomacromolecule into Porous Crystal of a Huge Protein Complex Hemocyanin (2017)
  • Author(s): Koji Kato, Asuka Matsuno, Yuxin Ye, Yuki Ohnishi, Akira Kitamura, Masataka Kinjo, Satoshi Abe, Takashi Ueda, Yoshikazu Tanaka, Min Yao
  • Organizer: 新学術領域研究「動的秩序と機能」第5回国際シンポジウム
  • Place of Presentation: 東京大学(東京都，目黒区)
  • Year and Date: 2017-01-21
  • Int'l Joint Research
• [Presentation] 巨大タンパク質会合体ヘモシアニンの多孔質性結晶を用いた生体分子の包摂 (2016)
  • Author(s): Asuka Matsuno, Ye Yuxin, Yuki Ohnishi, Akira Kitamura, Masataka Kinjo, Satoshi Abe, Takafumi Ueno, Yoshikazu Tanaka, Min Yao
  • Organizer: 第54回日本生物物理学会年会
  • Place of Presentation: つくば国際会議場(茨城県，つくば市)
  • Year and Date: 2016-11-25
• [Presentation] 超好熱性古細菌RNaseP構成タンパク質Rpp38のRNA活性化の構造基盤 (2016)
  • Author(s): 大嶋浩介，高緒柱，中島崇，田中良和，姚閔，木村誠
  • Organizer: 平成28年度日本結晶学会年会
  • Place of Presentation: 茨城県立県民文化センター(茨城県，水戸市)
  • Year and Date: 2016-11-17
• [Presentation] Pore formation mechanism of staphylococcal pore forming toxin (2016)
  • Author(s): Yoshikazu Tanaka
  • Organizer: Max Planck Institute of Molecular Physiology Department 3 Lab Retreat Seminar
  • Place of Presentation: Ringberg，ドイツ
  • Year and Date: 2016-10-09
  • Int'l Joint Research / Invited
• [Presentation] aEF-2 recognition mechanism of ribosomal aP1 stalk at GTPase-associated center of ribosome (2016)
  • Author(s): Takehito Tanzawa, Yuki Kumakura, Yoshikazu Tanaka, Toshio Uchiumi, Isao Tanaka, MinYao
  • Organizer: The 42nd NAITO CONFERENCE on In the Vanguard of Structural Biology: Revolutionizing Life Science
  • Place of Presentation: シャトレーゼガトーキングダム札幌 （北海道，札幌市)
  • Year and Date: 2016-10-04
  • Int'l Joint Research
• [Presentation] リボソームP1ストークによる翻訳伸長因子PhoEF-2認識機構の解明 (2016)
  • Author(s): 丹澤豪人，加藤公児，熊倉侑紀，田中良和，内海利男，田中勲，姚閔
  • Organizer: 第4回Ribosome Meeting
  • Place of Presentation: 大阪医科大学(大阪府，高槻市)
  • Year and Date: 2016-09-17
• [Presentation] バクテリアにおけるユビチキン様翻訳後修飾の構造基盤 (2016)
  • Author(s): 陳明皓，奈良井峻，大村直毅，鴫直樹，田中良和，姚閔
  • Organizer: RNAフロンティアミーティング2016
  • Place of Presentation: いこいの湯宿いろは(北海道，虻田郡ニセコ町)
  • Year and Date: 2016-08-31
• [Presentation] バクテリアにおける二機能性ユビキチン様タンパク質の機能調節の構造基盤 (2016)
  • Author(s): 陳明皓，奈良井峻，大村直毅，鴫直樹，田中良和，姚閔
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場(福岡県，福岡市)
  • Year and Date: 2016-06-07
• [Presentation] 超巨大蛋白質会合体ヘモシアニンの結晶構造（Crystal structure of supermolecule hemocyanin） (2016)
  • Author(s): 松野明日香，蓋作啓，加藤公児，田中良和，姚閔
  • Organizer: 2015年度量子ビームサイエンスフェスタ・第7回MLFシンポジウム・第33回PFシンポジウム
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
  • Year and Date: 2016-03-15
• [Presentation] Multidomain architecture of SepCysE confers transsulfursome flexibility to synthesize Cys-tRNACys in two-step indirect pathway (2016)
  • Author(s): Meirong Chen, Yume Kubo, Koji Kato, Yoshikazu Tanaka, Isao Tanaka, Min Yao
  • Organizer: 第53回日本生化学会北海道支部例会 日本生化学会北海道支部・日本生物物理学会北海道支部 合同シンポジウム
  • Place of Presentation: 北海道大学(北海道，札幌市)
• [Presentation] Investigating a novel sulfur transfer mechanism involving an [4Fe-4S] cluster and ubiquitin-like protein sulfur donor (2016)
  • Author(s): Minghao Chen, Shun Narai, Naoki Omura, Min Yao, Naoki Shigi and Yoshikazu Tanaka
  • Organizer: The 4th International Life-Science Symposium (ILSS)
  • Place of Presentation: 北海道大学(北海道，札幌市)
  • Int'l Joint Research
• [Presentation] Crystal structure of the intact 3.8-MDa molluscan hemocyanin (2015)
  • Author(s): Asuka Matsuno, Zuoqi Gai, Koji Kato, Sanae Kato, Takeshi Shimizu, Takeya Yoshioka, Hideki Kishimura, Tohru Terada, Yoshikazu Tanaka, Min Yao
  • Organizer: The 3rd International Life-Science Symposium
  • Place of Presentation: 北海道大学学術交流会館（北海道札幌市）
  • Year and Date: 2015-11-26
  • Int'l Joint Research
• [Presentation] The first crystal structure of intact 3.8 MDa molluscan hemocyanin (2015)
  • Author(s): 松野明日香，蓋作啓，加藤公児，加藤早苗，清水健志，吉岡武哉，岸村栄毅，寺田透，田中良和，姚閔
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 金沢大学角間キャンパス自然科学本館（石川県金沢市）
  • Year and Date: 2015-09-13
• [Presentation] The study on GTPase recognition mechanism of ribosomal P stalk on GTPase-associated center (2015)
  • Author(s): Takehito Tanzawa, Yuki Kumakura, Yoshikazu Tanaka, Toshio Uchiumi, Isao Tanaka, Min Yao
  • Organizer: The 10th International Conference on Ribosome Synthesis
  • Place of Presentation: ブリュッセル（ベルギー）
  • Year and Date: 2015-08-19
  • Int'l Joint Research
• [Presentation] リボソームストークと翻訳因子GTPaseの相互作用 (2015)
  • Author(s): 丹澤豪人，熊倉侑紀，田中良和，内海利男，田中勲，姚閔
  • Organizer: 第17回日本RNA学会年会
  • Place of Presentation: ホテルライフォート札幌（北海道札幌市）
  • Year and Date: 2015-07-15
• [Presentation] 超好熱性古細菌RNasePにおける構造安定化に関わるRNA-タンパク質間相互作用の解析 (2015)
  • Author(s): 大嶋浩介，中島崇，角田佳充，木村誠，田中良和，姚閔
  • Organizer: 第17回日本RNA学会年会
  • Place of Presentation: ホテルライフォート札幌（北海道札幌市）
  • Year and Date: 2015-07-15
• [Presentation] 黄色ブドウ球菌が赤血球を破壊する毒素の作用原理（Molecular mechanism of pore forming toxin from Staphylococcus aureus） (2015)
  • Author(s): 田中良和，山下大智，菅原宇希，金子淳，神尾好是，姚閔
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: あわぎんホール（徳島県徳島市）
  • Year and Date: 2015-06-24
  • Invited
• [Presentation] 軟体動物の超巨大酸素運搬蛋白質会合体ヘモシアニンのX線結晶構造解析（Crystal structure analysis of oxygen transporting supermolecule hemocyanin） (2015)
  • Author(s): 松野明日香，蓋作啓，加藤公児，加藤早苗，清水健志，吉岡武哉，岸村栄毅，寺田透，田中良和，姚閔
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: あわぎんホール（徳島県徳島市）
  • Year and Date: 2015-06-24
• [Presentation] 分子量4MDaの細胞外酸素運搬体ヘモシアニンの解離－再会合 (2014)
  • Author(s): 加藤早苗，Md. Rafiqul Islam Khan，吉岡武也，信太茂春，岸村栄毅，清水健志，田中良和
  • Organizer: 第87回 日本生化学会大会
  • Place of Presentation: 国立京都国際会館（京都市）
  • Year and Date: 2014-10-15 – 2014-10-18
• [Presentation] 黄色ブドウ球菌由来α-ヘモリジン単量体の結晶構造 (2014)
  • Author(s): 菅原宇希，山下大智，田中良和，金子淳，神尾好是，田中勲，姚閔
  • Organizer: 第52回 日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター（札幌市）
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] 結晶構造解析により明らかになった黄色ブドウ球菌由来膜孔形成毒素の分子機構 (2014)
  • Author(s): 田中良和，山下大智，菅原宇希，金子淳，神尾好是，田中勲，姚閔
  • Organizer: 第61回 トキシンシンポジウム
  • Place of Presentation: ルネッサンスリゾートナルト（鳴門市）
  • Year and Date: 2014-09-03 – 2014-09-05
• [Book] Essential タンパク質科学 第2章 (2016)
  • Author(s): 田中良和
  • Total Pages: 36
  • Publisher: 南江堂
• [Remarks] 北海道大学 X線構造生物学研究室 ホームページ
  • URL: http://altair.sci.hokudai.ac.jp/g6/
• [Patent(Industrial Property Rights)] ヘモシアニン会合体を用いた包摂体の製造方法 (2016)
  • Inventor(s): 田中良和，松野明日香，北村朗，金城政孝，姚閔，上野隆史，安部聡
  • Industrial Property Rights Holder: 国立大学法人北海道大学，国立大学法人東京工業大学
  • Industrial Property Rights Type: 特許
  • Filing Date: 2016-06-01