• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Crystallographic studies of macromolecular complexes in transcription and translation : RNA polymerases and the ribosome

Research Project

Project/Area Number 20247008
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionThe Institute of Physical and Chemical Research (2010-2011)
The University of Tokyo (2009)
Tokyo Gakugei University (2008)

Principal Investigator

YOKOYAMA Shigeyuki  独立行政法人理化学研究所, 生命分子システム基盤研究領域, 領域長 (00159229)

Co-Investigator(Kenkyū-buntansha) SEKINE Shunichi  東京大学, 大学院・理学系研究科, 講師 (50321774)
ITO Takuhiro  東京大学, 大学院・理学系研究科, 助教 (70401164)
FUJII Yoshifumi  東京大学, 大学院・理学系研究科, 特任助教 (30392096)
Co-Investigator(Renkei-kenkyūsha) SEKINE Shunichi  東京大学, 大学院・理学系研究科, 講師 (50321774)
ITO Takuhiro  東京大学, 大学院・理学系研究科, 助教 (70401164)
FUJII Yoshifumi  東京大学, 大学院・理学系研究科, 特任助教 (30392096)
Project Period (FY) 2008 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥43,290,000 (Direct Cost: ¥33,300,000、Indirect Cost: ¥9,990,000)
Fiscal Year 2011: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Fiscal Year 2010: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Fiscal Year 2009: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Fiscal Year 2008: ¥14,820,000 (Direct Cost: ¥11,400,000、Indirect Cost: ¥3,420,000)
Keywords転写 / RNAポリメラーゼ / 転写因子 / 翻訳 / リボソーム / 翻訳開始因子 / X線結晶構造解析
Research Abstract

To approach the structural basis of transcription and translation, we carried out structural studies on RNA polymerase and ribosome, which play a central role in transcription and translation, respectively. These include RNA polymerase bound with regulatory proteins and nucleic acids and small ribosomal subunit bound with regulatory proteins and RNA. We also established preparation method of eukaryotic proteins responsible for transcription or translation, and performed crystallography.

Report

(5 results)
  • 2011 Final Research Report ( PDF )
  • 2010 Annual Research Report   Self-evaluation Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (56 results)

All 2012 2011 2010 2009 2008

All Journal Article (32 results) (of which Peer Reviewed: 32 results) Presentation (24 results)

  • [Journal Article] Structural basis of transcription by bacterial and eukaryotic RNA polymerases2012

    • Author(s)
      Sekine, S., Tagami, S. and Yokoyama, S.
    • Journal Title

      Curr. Opin. Struct. Biol.

      Volume: 22 Pages: 110-118

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA Polymerase III2011

    • Author(s)
      Ehara, H., Sekine, S. and Yokoyama, S.
    • Journal Title

      Protein Sci

      Volume: 20 Pages: 1558-1565

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A novel conformation of RNA polymerase sheds light on the mechanism of transcription2011

    • Author(s)
      Tagami, S., Sekine, S. and Yokoyama, S.
    • Journal Title

      Transcription

      Volume: 2 Pages: 162-167

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein2010

    • Author(s)
      Tagami, S., Sekine, S., Kumarevel, T., Hino, N., Murayama, Y., Kamegamori, S., Yamamoto, M., Sakamoto, K. and Yokoyama, S.
    • Journal Title

      Nature

      Volume: 468 Pages: 978-982

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase2010

    • Author(s)
      Hikida, Y., Kuratani, M., Bessho, Y., Sekine, SI. and Yokoyama, S.
    • Journal Title

      Acta Crystallogr. D Biol. Crystallogr

      Volume: 66(12) Pages: 1301-1307

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Codon Reassignment in the Escherichia coli Genetic Code2010

    • Author(s)
      Mukai, T., Hayashi, A., Iraha, F., Sato, A., Ohtake, K., Yokoyama, S. and Sakamoto, K.
    • Journal Title

      Nucleic Acids Res

      Volume: 38 Pages: 8188-8195

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin2010

    • Author(s)
      Kuratani, M., Hirano, M., Goto-Ito, S., Itoh, Y., Hikida, Y., Nishimoto, M., Sekine, SI., Bessho, Y., Ito, T., Grosjean, H. and Yokoyama, S.
    • Journal Title

      J. Mol. Biol

      Volume: 401(3) Pages: 323-333

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine2010

    • Author(s)
      Chiba, S., Itoh, Y., Sekine, S. and Yokoyama, S.
    • Journal Title

      Mol. Cell

      Volume: 39 Pages: 410-420

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structurally Designed Trans-2-phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM12010

    • Author(s)
      Mimasu, S., Sato, S., Umezawa, N., Higuchi, T., Umehara, T. and Yokoyama, S.
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 6494-6503

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions2010

    • Author(s)
      Ito, T. and Yokoyama, S.
    • Journal Title

      Nature

      Volume: 467 Pages: 612-616

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure of Nondiscriminating Glutamyl-tRNA Synthetase from Thermotoga maritime2010

    • Author(s)
      Ito, T., Kiyasu, N., Matsunaga, R., Takahashi, S. and Yokoyama, S.
    • Journal Title

      Acta Crystallogr. D Biol. Crystallogr

      Volume: 66(7) Pages: 813-820

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] The C-terminal BAG Domain of BAG5 Induces Conformational Changes of the Hsp70 Nucleotide-binding Domain for ADP-ATP Exchange2010

    • Author(s)
      Arakawa, A., Handa, N., Ohsawa, N., Shida, M., Kigawa, T., Hayashi, F., Shirouzu, M. and Yokoyama, S.
    • Journal Title

      Structure

      Volume: 18 Pages: 309-319

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh12010

    • Author(s)
      Tagami, S., Sekine, SI., Kumarevel, T., Yamamoto, M. and Yokoyama, S.
    • Journal Title

      Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun

      Volume: 66(1) Pages: 64-68

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.2010

    • Author(s)
      Tagami, S., Sekine, S., Kumarevel, T., Hino, N., Murayama, Y., Kamegamori, S., Yamamoto, M., Sakamoto, K., Yokoyama, S.
    • Journal Title

      Nature 468

      Pages: 978-982

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.2010

    • Author(s)
      Ito, T., Yokoyama, S.
    • Journal Title

      Nature 467

      Pages: 612-616

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.2010

    • Author(s)
      Chiba, S., Itoh, Y., Sekine, S., Yokoyama, S.
    • Journal Title

      Mol.Cell 39

      Pages: 410-420

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.2010

    • Author(s)
      Tagami, S., et al.
    • Journal Title

      Nature

      Volume: 468 Pages: 978-982

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima.2010

    • Author(s)
      Ito, T., et al.
    • Journal Title

      Acta.Crystallogr.D Biol.Crystallogr.

      Volume: 66 Pages: 813-820

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.2010

    • Author(s)
      Ito, T., et al.
    • Journal Title

      Nature

      Volume: 467 Pages: 612-616

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the major role of O-Phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.2010

    • Author(s)
      Chiba, S., et al.
    • Journal Title

      Mol.Cell

      Volume: 39 Pages: 410-420

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.2010

    • Author(s)
      Kuratani, M., et al.
    • Journal Title

      J.Mol.Biol.

      Volume: 401 Pages: 323-333

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-Methyltransferase.2010

    • Author(s)
      Hikida, Y., et al.
    • Journal Title

      Acta Crystallogr.D Biol.Crystallogr.

      Volume: 66 Pages: 1301-1307

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1.2010

    • Author(s)
      Tagami S, Sekine S, Kumarevel T, Yamamoto M, Yokoyama S.
    • Journal Title

      Acta Crystallogr.Sect F. 66

      Pages: 64-68

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of theαsubunit of human translation initiation factor 2B2009

    • Author(s)
      Hiyama, T. B., Ito, T., Imataka, H. and Yokoyama, S.
    • Journal Title

      J. Mol. Biol

      Volume: 392 Pages: 937-951

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation2009

    • Author(s)
      Goto-Ito, S., Ito, T., Kuratani, M., Bessho, Y. and Yokoyama, S.
    • Journal Title

      Nat. Struct. Mol. Biol

      Volume: 16 Pages: 1109-1115

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of human selenocysteine tRNA2009

    • Author(s)
      Itoh, Y., Chiba, S., Sekine, SI. and Yokoyama, S.
    • Journal Title

      Nucleic Acids Res

      Volume: 37 Pages: 6259-6268

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization2009

    • Author(s)
      Naganuma, M., Sekine, SI., Fukunaga, R. and Yokoyama, S.
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 106 Pages: 8489-8494

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs2009

    • Author(s)
      Itoh, Y., Sekine, SI., Matsumoto, E., Akasaka, R., Takemoto, C., Shirouzu, M. and Yokoyama, S.
    • Journal Title

      J. Mol. Biol

      Volume: 385 Pages: 1456-1469

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the α subunit of human translation initiation factor 2B.2009

    • Author(s)
      Hiyama, T.B., Ito, T., Imataka, H., Yokoyama, S.
    • Journal Title

      J.Mol.Biol. 392

      Pages: 937-951

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.2009

    • Author(s)
      Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S.
    • Journal Title

      Proc.Natl.Acad.Sci.U.S.A. 106

      Pages: 8489-8494

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Crystal Structure of the alpha subunit of human translation initiation factor 2B2009

    • Author(s)
      Hiyama, T.B., Ito, T., Imataka, H., Yokoyama, S
    • Journal Title

      J Mol Biol 392

      Pages: 937-951

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog2008

    • Author(s)
      Oki, K., Sakamoto, K., Kobayashi, T., Sasaki, H. M. and Yokoyama, S.
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 105 Pages: 13298-13303

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Presentation] Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein2011

    • Author(s)
      Yokoyama, S
    • Organizer
      FASEB Summer Research Conferences Mechanism & Regulation of Procaryotic Transcription
    • Place of Presentation
      Saxtons River, USA
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystal Structure of theαSubunit of Human Eukaryotic Initiation Factor 2B2011

    • Author(s)
      Hiyama, T. B.
    • Organizer
      RNA2011
    • Place of Presentation
      Kyoto
    • Related Report
      2011 Final Research Report
  • [Presentation] RNAポリメラーゼの新規コンフォメーションと機能の関係2011

    • Author(s)
      田上俊輔
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      大阪市
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystallographic Studies of Aminoacyl-tRNA Synthesis and tRNA Modification2010

    • Author(s)
      Itoh, Y., Chiba, S., Naganuma, M., Goto-ito, S., Fukunaga, R., Kuratani, M., Bessho, Y., Ito, T., Sekine, SI., Yokoyama, S.
    • Organizer
      23rd tRNA Workshop
    • Place of Presentation
      Aveiro, Portugal
    • Year and Date
      2010-01-29
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] グルタミン-トランスアミドソームの結晶構造解析2010

    • Author(s)
      伊藤拓宏
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2011 Final Research Report
  • [Presentation] X-ray crystal structure of okadaic acid binding protein 2.12010

    • Author(s)
      江原晴彦
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2011 Final Research Report
  • [Presentation] RNAポリメラーゼの新規構造状態:トランスロケーションと転写制御のメカニズム解明への手掛り2010

    • Author(s)
      田上俊輔
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2011 Final Research Report
  • [Presentation] 翻訳開始因子eIF2Bαによるリン酸基認識機構の研究2010

    • Author(s)
      檜山卓也
    • Organizer
      第12回RNAミーティング
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] O-ホスホセリルtRNAキナーゼとセレノシステインtRNA複合体の結晶構造2010

    • Author(s)
      伊藤弓弦
    • Organizer
      第12回RNAミーティング
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] アラニルtRNA合成酵素によるG・U塩基対認識の構造基盤2010

    • Author(s)
      永沼政広
    • Organizer
      第12回RNAミーティング
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] グルタミン-トランスアミドソームの結晶構造解析2010

    • Author(s)
      伊藤拓宏
    • Organizer
      第12回RNAミーティング
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] RNAポリメラーゼの新規コンフォメーション状態2010

    • Author(s)
      田上俊輔
    • Organizer
      第12回RNAミーティング
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] RNAポリメラーゼの新規構造状態:トランスロケーションと転写制御のメカニズム解明への手掛り2010

    • Author(s)
      田上俊輔
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2010 Annual Research Report
  • [Presentation] X-ray crystal structure of okadaic acid binding protein 2.12010

    • Author(s)
      江原晴彦
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2010 Annual Research Report
  • [Presentation] ゲルタミン-トランスアミドソームの結晶構造解析2010

    • Author(s)
      伊藤拓宏
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会(BMB2010)
    • Place of Presentation
      神戸
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural biology and engineering of the transcription and translation systems2009

    • Author(s)
      Yokoyama, S.
    • Organizer
      International Symposium "Membranes and Modules"
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2009-12-10
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Structural basis of transcription regulation revealed by the crystal structure of Thermus thermophilus RNA polymerase elongation complex bound with a transcriptional regulator Gfh12009

    • Author(s)
      関根俊一
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystal structure of an RNA polymerase translocation intermediate2009

    • Author(s)
      田上俊輔
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural basis of transcription regulation revealed by the crystal structure of Thermus thermophilus RNA polymerase elongation complex bound with a transcriptional regulator Gfh1.2009

    • Author(s)
      関根俊一、田上俊輔、Thirumananseri Kumarevel、横山茂之
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2009 Annual Research Report
  • [Presentation] Crystal structure of an RNA polymerase translocation intermediate.2009

    • Author(s)
      田上俊輔、関根俊一、Thirumananseri Kumarevel、横山茂之
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2009 Annual Research Report
  • [Presentation] Crystallography of bacterial RNA polymerase complexed with transcription factors2008

    • Author(s)
      田上俊輔
    • Organizer
      XXI Congress of the international Union of Crystallography(IUCr2008)
    • Place of Presentation
      大阪
    • Year and Date
      2008-08-23
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystallography of bacterial RNA polymerase complexed with transcription factors2008

    • Author(s)
      田上俊輔
    • Organizer
      XXI Congress of the international Union of Crystallography (IUCr2008)
    • Place of Presentation
      大阪国際会議場
    • Year and Date
      2008-08-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] 翻訳開始因子eIF2B□のX線結晶構造解析2008

    • Author(s)
      檜山卓也
    • Organizer
      第10回日本RNA学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2008-07-23
    • Related Report
      2011 Final Research Report
  • [Presentation] 翻訳開始因子eIF2BαのX線結晶構造解析2008

    • Author(s)
      檜山卓也
    • Organizer
      第10回日本RNA学会年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2008-07-23
    • Related Report
      2008 Annual Research Report

URL: 

Published: 2008-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi