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2001 Fiscal Year Final Research Report Summary

Crystallographics study of active ion transport

Research Project

Project/Area Number 11308026
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo

Principal Investigator

TOYOSHIMA Chikashi  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Professor, 分子細胞生物学研究所, 教授 (70172210)

Co-Investigator(Kenkyū-buntansha) OGAWA Haruo  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Research associate, 分子細胞生物学研究所, 助手 (40292726)
NAKASAKO Masayoshi  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Lecturer, 分子細胞生物学研究所, 講師 (30227764)
Project Period (FY) 1999 – 2001
Keywordsactive transport / Protein crystals / membrane proteins / ion pump / electron crystallography / X-ray crystallography / ATPase
Research Abstract

The first goal of this research was to determine the atomic structure of the Ca^<2+>-ATPase of sarcoplasmic reticulum, a representative member of P-type ion translocating ATPases, using very thin 3D crystals of X-ray quality that we generated in the presence of calcium. The next goal was to crystallise the enzyme in other different physiological conditions. This research proceeded much faster than we had expected. We have already obtained atomic models for 3 different physiological states (ElCa^<2+>, E2 and E2P) and have succeeded in crystallising the enzyme in two other states (E1ATP and E1P analogues). The atomic models revealed structural changes accompanying the dissociation of Ca^<2+> and phosphate. That is, 6 out of 10 transmembrane α-helices undergo a large scale rearrangements and 3 cytoplasmic domains, which are widely separated with bound Ca^<2+>, gather to form a compact single headpiece when calcium ions dissociate. Two of the transmembrane helices show movements that contain large components normal to the membrane plane. These helices move like pistons on the binding and release of Ca^<2+> and the cytoplasmic domains serve as a energy converter that drives the pistons. Thus, our results indicate that P-type ion translocating ATPases have a mechanism like mechanical pumps at an atomic scale.
Some parts of these results were published in Nature in June 2000 and August 2002, and in PNAS in December 2002. These publications have collected considerable interests and been reviewed in detail in News and Views of Nature and Nature Structure Biology and in Editor's choice of Science. The results have been introduced already into world-standard text books of biochemistry and molecular biology.

  • Research Products

    (52 results)

All Other

All Publications (52 results)

  • [Publications] C.Toyoshima: "Structural changes in the calcium pump accompanying the dissociation of calcium"Nature. 418. 605-611 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] H.Ogawa: "Homology modeling of the cation binding sites of Na^+K^+-AT Pase"Proc. Nat. Acad. Sci. USA. 99. 15977-15982 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] S.Hua: "Functional role of "N" (Nucleotide) and "P" (Phosphorylation) domain interactions in the sarcoplasmic reticulum (SERCA) ATPase"Biochemistry. 41. 2264-2272 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] S.Hua: "Fe^<2+> Catalyzed oxidation and cleavage of sarcoplasmic reticulum ATPase reveals Mg^<2+> and M^<2+>-ATP sites"Biochemistry. 41. 11405-11410 (2002)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] S.Danko: "Organization of cytoplasmic domains of sarcoplasmic reticulum Ca^<2+>-ATPase in E1P and E1ATP states : a limited proteolysis study"FEBS letters. 505. 129-135 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] S.Danko: "ADP-insensitive phosphoenzyme intermediate of sarcoplasmic reticulum Ca2+-ATPase has a compact conformation resistant to proteinase K, V8 protease and trypsin"FEBS letters. 489. 277-282 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Z.Zhang: "The role of the M6-M7 Loop (L67) in stabilization of the phosphorylation and Ca^<2+> binding domains of the sarcoplasmic reticulum Ca^<2+>-ATPase (SERCA)"J. Biol. Chem.. 276. 15232-15239 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] C.Toyoshima: "Crystal structure of the calcium pump of sarcoplasmi reticulum at 2.6 A resolution"Nature. 405. 647-655 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] C.Toyoshima: "Structure determination of tubular crystals of membrane proteins. I. Indexing of diffraction patterns"Ultramicroscopy. 84. 1-14 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] K.Yonekura: "Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes"Ultramicroscopy. 84. 15-28 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] K.Yonekura: "Structure determination of tubular crystals of membrane proteins. III. Solvent flattening"Ultramicroscopy. 84. 29-45 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] H.Ogawa: "Soluble P-type ATPase from an archaeon, Methanococcus jannaschii"FEBS letters. 471. 99-102 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Z.Zhang: "Detailed characterization of the cooperative mechanism of Ca^<2+> binding and catalytic activation in the Ca^<2+> transport (SERCA) ATPase"Biochemistry. 39. 8758-8767 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] S.Hua: "Distinct topologies of mono-and decavanadate binding and photo-oxidative cleavage in the sarcoplasmic reticulum ATPase"J. Biol. Chem.. 275. 30546-30550 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] K.Hirose: "Structural comparison of dimeric Eg5, Neurospora Kinesin (Nkin) and Ncd Head-Nkin Neck chimera with conventional Kinesin"EMBO Journal. 19. 5308-5314 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "筋小胞体カルシウムポンプの構造決定"蛋白質・核酸・酵素. 46. 1374-1380 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "カルシウムポンプの構造と能動輸送のメカニズム"現代化学. 365. 22-28 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "筋小胞体カルシウムポンプの構造決定"日本放射光学会誌. 14. 42-48 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "カルシウムポンプの結晶構造"細胞工学. 19. 1517-1519 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "膜タンパク質を見る"バイオサイエンスとインダストリー. 58. 9-10 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 江橋節郎: "カルシウムポンプの構造決定"パリティー. 15. 122-124 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 中迫雅由: "筋小胞体カルシウムポンプの結晶構造解析"日本結晶学会誌. 42. 478-485 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 小川治夫: "チャネルの立体構造決定法I"脳の科学. 21. 997-1004 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 小川治夫: "チャネルの立体構造決定法II"脳の科学. 21. 1121-1128 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 豊島 近: "イオンチャネル、ポンプの構造と機能"蛋白質・核酸・酵素. 44. 557-565 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] E.Carafoli, J.Krebs: "Calcium Homeostasis (Topics in Biological Inorganic Chemistry Vol. 3)"Springer-Verlag, Berlin. (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] C. Toyoshima: "Structural changes in the calcium pump accompanying the dissociation of calcium"Nature. 418. 605-611 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] H. Ogawa: "Homology modeling of the cation binding sites of Na^+ K^+-ATPase"Proc. Nat. Acad. Sci. USA. 99. 15977-15982 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Hua: "Functional role of "N" (Nucleotide) and "P" (Phosphorylation) domain interactions in the sarcoplasmic reticulum (SERCA) ATPase."Biochemistry. 41. 2264-2272 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Hua: "Fe^<2+>-catalyzed oxidation and cleavage of sarcoplasmic reticulum ATPase reveals Mg^<2+> and Mg^<2+>-ATP sites"Biochemistry. 41. 11405-11410 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Danko: "Organization of cytoplasmic domains of sarcoplasmic reticulum Ca^<2+>-ATPase in E1P and E1ATP states: a limited proteolysis study."FEBS letters. 505. 129-13 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Danko: "ADP-insensitive phosphoenzyme intermediate of sarcoplasmic reticulum Ca^<2+>-ATPase has a compact conformation resistant to proteinase K, V8 protease and trypsin"FEBS letters. 489. 277-2829 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Z. Zhang: "The role or the M6-M7 Loop (L67) in stabilization of the phosphorylation and Ca^<2+> binding domains of the sarcoplasmic reticulum Ca^<2+>-ATPase (SERCA)"J. Biol. Chem.. 276. 15232-15239 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution"Nature. 405. 647-655 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Structure determination of tubular crystals of membrane proteins. I. Indexing of diffraction patterns"Ultramicroscopy. 84. 1-14 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] K. Yonekura: "Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes"Ultramicroscopy. 84. 15-28 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] K. Yonekura: "Structure determination of tubular crystals of membrane proteins. III. Solvent flattening."Ultramicroscopy. 84. 29-45 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] H. Ogawa: "Soluble P-type ATPase from an archaeon, Methanococcus jannaschii."FEES letters. 471. 99-102 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Z. Zhang: "Detailed characterization of the cooperative mechanism of Ca^<2+> binding and catalytic activation in the Ca^<2+> transport (SERCA) ATPase."Biochemistry. 39. 8758-8767 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Hua: "Distinct topologies of mono-and decavanadate binding and photo-oxidative cleavage in the sarcoplasmic reticulum ATPase"J. Biol. Chem.. 275. 30546-30550 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] K. Hirose: "Structural comparison of dimeric Eg5, Neurospora Kinesin (Nkin) and Ncd Head-Nkin Neck chimera with conventional Kinesin"EMBO Journal. 19. 5308-5314 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] G. Inesi: "The Ca^<2+> pump of sarco-and endoplasmic reticulum membranes"Calcium Homeostasis (Topics in Biological Inorganic Chemistry Vol. 3)eds. E. Carafoli and J. Krebs(Springer-Verlag, Berlin). 143-154 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Structure determination of the calcium pump of sarcoplasmic reticulum (in Japanese)"Protein, Nucleic Acid and Enzyme. 46. 1374-1380 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Structure of calcium pump and the mechanism of active transport (in Japanese)"Modern Chemistry. 365. 22-28 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Structure determination of the calcium pump of sarcoplasmic reticulum (in Japanese)"Journal of the Japanese Society for Synchrotron Radiation Research. 14. 42-48 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Crystal structure of the calcium pump (in Japanese)"Cell Technology. 19. 1517-1519 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Visualizing membrane proteins (in Japanese)"Bioscience & Industry. 58. 9-10 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] S. Ebashi: "Structure determination of the calcium pump (in Japanese)"Parity. 15. 122-124 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] M. Nakasako: "Structure determination of the calcium pump of sarcoplasmic reticulum (in Japanese)"Journal of the Crystallographic Society of Japan. 42. 478-485 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] H. Ogawa: "Methods for structure determination of channels I (in Japanese)"Brain Science. 21. 997-1004 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] H. Ogawa: "Methods for structure determination of channels II (in Japanese)"Brain Science. 21. 1121-1128 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] C. Toyoshima: "Structures and functions of ion channels and pumps (in Japanese)"Protein, Nucleic Acid and Enzyme. 44. 557-565 (1999)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2003-09-17  

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