Ryuichiro Ishitani

Ryuichiro Ishitani

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Ryuichiro Ishitani

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Crystal structure of plant vacuolar iron transporter VIT1.

Nat Plants 2019 Mar 11;5(3):308-315. Epub 2019 Feb 11.

Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1038/s41477-019-0367-2DOI Listing
March 2019

Structural Basis of H-Dependent Conformational Change in a Bacterial MATE Transporter.

Structure 2019 Feb 15;27(2):293-301.e3. Epub 2018 Nov 15.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09692126183036
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http://dx.doi.org/10.1016/j.str.2018.10.004DOI Listing
February 2019

Cap-specific terminal -methylation of RNA by an RNA polymerase II-associated methyltransferase.

Science 2019 01 22;363(6423). Epub 2018 Nov 22.

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

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http://dx.doi.org/10.1126/science.aav0080DOI Listing
January 2019

Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.

Acta Crystallogr F Struct Biol Commun 2018 Dec 30;74(Pt 12):810-816. Epub 2018 Nov 30.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1107/S2053230X18016369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277958PMC
December 2018

An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin.

Biophys J 2018 Oct 27;115(7):1281-1291. Epub 2018 Aug 27.

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.08.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170652PMC
October 2018

Vibrational and Molecular Properties of Mg Binding and Ion Selectivity in the Magnesium Channel MgtE.

J Phys Chem B 2018 Oct 10;122(42):9681-9696. Epub 2018 Oct 10.

Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science , National Institutes of Natural Sciences , 38 Nishigo-Naka , Myodaiji, Okazaki 444-8585 , Japan.

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http://dx.doi.org/10.1021/acs.jpcb.8b07967DOI Listing
October 2018

Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1.

Nat Commun 2018 10 24;9(1):4424. Epub 2018 Oct 24.

Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

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http://dx.doi.org/10.1038/s41467-018-06922-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200793PMC
October 2018

Free Energy Landscape for the Entire Transport Cycle of Triose-Phosphate/Phosphate Translocator.

Structure 2018 Sep 28;26(9):1284-1296.e4. Epub 2018 Jun 28.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.str.2018.05.012DOI Listing
September 2018

Structural basis for xenobiotic extrusion by eukaryotic MATE transporter.

Nat Commun 2017 11 21;8(1):1633. Epub 2017 Nov 21.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/s41467-017-01541-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696359PMC
November 2017

Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity.

Nat Plants 2017 Oct 2;3(10):825-832. Epub 2017 Oct 2.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/s41477-017-0022-8DOI Listing
October 2017

Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel.

Nat Commun 2017 10 12;8(1):876. Epub 2017 Oct 12.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/s41467-017-00887-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638823PMC
October 2017

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.

Mol Cell 2017 Aug 3;67(4):633-645.e3. Epub 2017 Aug 3.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.06.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957536PMC
August 2017

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1.

Mol Cell 2017 Jul 6;67(1):139-147.e2. Epub 2017 Jun 6.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.04.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957533PMC
July 2017

Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA.

Annu Rev Biochem 2017 06 7;86:541-566. Epub 2017 Apr 7.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; email: ,

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http://dx.doi.org/10.1146/annurev-biochem-061516-044813DOI Listing
June 2017

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.

Mol Cell 2017 Mar;65(6):1109-1121.e3

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173012
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http://dx.doi.org/10.1016/j.molcel.2017.02.007DOI Listing
March 2017

Structural insights into the nucleotide base specificity of P2X receptors.

Sci Rep 2017 03 23;7:45208. Epub 2017 Mar 23.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/srep45208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5362899PMC
March 2017

Breakpoint Cluster Region-Mediated Inflammation Is Dependent on Casein Kinase II.

J Immunol 2016 10 14;197(8):3111-3119. Epub 2016 Sep 14.

Division of Molecular Neuroimmunology, Institute for Genetic Medicine and Graduate School of Medicine, Hokkaido University, Sapporo 080-0615, Japan;

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http://dx.doi.org/10.4049/jimmunol.1601082DOI Listing
October 2016

Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA.

Cell 2016 Oct 29;167(2):484-497.e9. Epub 2016 Sep 29.

Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.09.002DOI Listing
October 2016

Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide.

Sci Rep 2016 10 10;6:34756. Epub 2016 Oct 10.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/srep34756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056382PMC
October 2016

Recent structural studies on Dom34/aPelota and Hbs1/aEF1α: important factors for solving general problems of ribosomal stall in translation.

Biophysics (Nagoya-shi) 2013 7;9:131-40. Epub 2013 Sep 7.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.2142/biophysics.9.131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629679PMC
August 2016

Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide.

Nat Commun 2016 08 8;7:12383. Epub 2016 Aug 8.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/ncomms12383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979064PMC
August 2016

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae.

Acta Crystallogr F Struct Biol Commun 2016 07 22;72(Pt 7):552-7. Epub 2016 Jun 22.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S2053230X16008931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933005PMC
July 2016

Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization.

Nat Commun 2016 07 15;7:12198. Epub 2016 Jul 15.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/ncomms12198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947182PMC
July 2016

Data processing pipeline for serial femtosecond crystallography at SACLA.

J Appl Crystallogr 2016 Jun 18;49(Pt 3):1035-1041. Epub 2016 Apr 18.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S1600576716005720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886989PMC
June 2016

Structural basis for amino acid export by DMT superfamily transporter YddG.

Nature 2016 06 30;534(7607):417-20. Epub 2016 May 30.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/nature17991DOI Listing
June 2016

Structural basis for specific inhibition of Autotaxin by a DNA aptamer.

Nat Struct Mol Biol 2016 05 4;23(5):395-401. Epub 2016 Apr 4.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1038/nsmb.3200DOI Listing
May 2016

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.

Cell 2016 May 21;165(4):949-62. Epub 2016 Apr 21.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899970PMC
May 2016

Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening.

PLoS One 2015 26;10(6):e0131094. Epub 2015 Jun 26.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131094PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482709PMC
April 2016

Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9.

Mol Cell 2016 Mar;61(6):886-94

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://www.cell.com/molecular-cell/pdf/S1097-2765(16)00129-5
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http://dx.doi.org/10.1016/j.molcel.2016.02.018DOI Listing
March 2016

Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.

Biophys J 2016 Mar;110(6):1346-54

Theoretical Molecular Science Laboratory, RIKEN, Wako, Saitama, Japan; Interdisciplinary Theoretical Science Research Group (iTHES), RIKEN, Wako, Saitama, Japan; Quantitative Biology Center, RIKEN, Kobe, Hyogo, Japan; Advanced Institute for Computational Science, RIKEN, Kobe, Hyogo, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.01.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816688PMC
March 2016

Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels.

Cell Rep 2016 Feb 21;14(4):932-944. Epub 2016 Jan 21.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.087DOI Listing
February 2016

Structure and Engineering of Francisella novicida Cas9.

Cell 2016 Feb 11;164(5):950-61. Epub 2016 Feb 11.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.01.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899972PMC
February 2016

Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State.

Cell Rep 2015 Nov 12;13(8):1561-8. Epub 2015 Nov 12.

Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.10.025DOI Listing
November 2015

Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin.

Nat Commun 2015 Oct 13;6:8545. Epub 2015 Oct 13.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/ncomms9545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4633820PMC
October 2015

Crystal Structure of Staphylococcus aureus Cas9.

Cell 2015 Aug;162(5):1113-26

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670267PMC
August 2015

Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase.

Structure 2015 May 9;23(5):843-850. Epub 2015 Apr 9.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://www.cell.com/structure/pdf/S0969-2126(15)00078-7.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S096921261500078
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http://dx.doi.org/10.1016/j.str.2015.01.023DOI Listing
May 2015

Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK.

Nat Commun 2015 May 11;6:7097. Epub 2015 May 11.

1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/ncomms8097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432589PMC
May 2015

Atomistic design of microbial opsin-based blue-shifted optogenetics tools.

Nat Commun 2015 May 15;6:7177. Epub 2015 May 15.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/ncomms8177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479019PMC
May 2015

Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom.

Cell Rep 2015 Apr 9;11(3):366-75. Epub 2015 Apr 9.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.03.030DOI Listing
April 2015

Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter.

Nat Commun 2015 Jan 19;6:6112. Epub 2015 Jan 19.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/ncomms7112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309421PMC
January 2015

Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase.

Sci Rep 2014 Dec 3;4:7299. Epub 2014 Dec 3.

1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/srep07299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252904PMC
December 2014

Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2+ channel MgtE.

Nat Commun 2014 Nov 4;5:5374. Epub 2014 Nov 4.

1] Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/ncomms6374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241985PMC
November 2014

The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.

Nucleic Acids Res 2014 Oct 1;42(19):12295-305. Epub 2014 Oct 1.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan

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http://dx.doi.org/10.1093/nar/gku898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231759PMC
October 2014

Conformational variation of the translocon enhancing chaperone SecDF.

J Struct Funct Genomics 2014 Sep 25;15(3):107-15. Epub 2013 Dec 25.

BRI and ITRI, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568, Japan,

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http://dx.doi.org/10.1007/s10969-013-9168-4DOI Listing
September 2014

Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation.

Acta Crystallogr F Struct Biol Commun 2014 Sep 27;70(Pt 9):1236-9. Epub 2014 Aug 27.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S2053230X14015726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157426PMC
September 2014

Structural and functional analyses of DNA-sensing and immune activation by human cGAS.

PLoS One 2013 7;8(10):e76983. Epub 2013 Oct 7.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan ; Global Research Cluster, RIKEN, Wako, Saitama, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076983PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792152PMC
August 2014

Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP.

Acta Crystallogr F Struct Biol Commun 2014 Aug 23;70(Pt 8):1009-14. Epub 2014 Jul 23.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://journals.iucr.org/f/issues/2014/08/00/tb5070/tb5070.p
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http://scripts.iucr.org/cgi-bin/paper?S2053230X14014046
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http://dx.doi.org/10.1107/S2053230X14014046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118794PMC
August 2014

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans.

Acta Crystallogr F Struct Biol Commun 2014 Aug 23;70(Pt 8):1056-60. Epub 2014 Jul 23.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1107/S2053230X14012540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118803PMC
August 2014

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6.

Acta Crystallogr F Struct Biol Commun 2014 Jun 24;70(Pt 6):794-9. Epub 2014 May 24.

Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S2053230X14008929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051540PMC
June 2014

Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases.

Nucleic Acids Res 2014 May 1;42(9):6052-63. Epub 2014 Apr 1.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan

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http://dx.doi.org/10.1093/nar/gku234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027206PMC
May 2014

Structural basis of Sec-independent membrane protein insertion by YidC.

Nature 2014 May 16;509(7501):516-20. Epub 2014 Apr 16.

1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/nature13167DOI Listing
May 2014

Crystal structure of a claudin provides insight into the architecture of tight junctions.

Science 2014 Apr;344(6181):304-7

Cellular and Structural Physiology Institute, Nagoya University, Chikusa, Nagoya 464-8601, Japan.

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http://dx.doi.org/10.1126/science.1248571DOI Listing
April 2014

Structural basis for potent inhibition of SIRT2 deacetylase by a macrocyclic peptide inducing dynamic structural change.

Structure 2014 Feb 2;22(2):345-52. Epub 2014 Jan 2.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.str.2013.12.001DOI Listing
February 2014

Crystal structure of Cas9 in complex with guide RNA and target DNA.

Cell 2014 Feb 13;156(5):935-49. Epub 2014 Feb 13.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139937PMC
February 2014

Screening and X-ray crystal structure-based optimization of autotaxin (ENPP2) inhibitors, using a newly developed fluorescence probe.

ACS Chem Biol 2013 Aug 3;8(8):1713-21. Epub 2013 Jun 3.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1021/cb400150cDOI Listing
August 2013

Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger.

Science 2013 Jul 23;341(6142):168-72. Epub 2013 May 23.

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1126/science.1239002DOI Listing
July 2013

Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT.

Proc Natl Acad Sci U S A 2013 Jul 24;110(28):11343-8. Epub 2013 Jun 24.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan.

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http://dx.doi.org/10.1073/pnas.1301079110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710879PMC
July 2013

[Structural biology of ubiquitin signaling].

Seikagaku 2013 Jun;85(6):423-9

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032.

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June 2013

Backbone resonance assignments for the cytoplasmic region of the Mg(2+) transporter MgtE in the Mg (2+)-unbound state.

Biomol NMR Assign 2013 Apr 5;7(1):93-6. Epub 2012 Apr 5.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

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http://dx.doi.org/10.1007/s12104-012-9385-yDOI Listing
April 2013

The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO).

J Biol Chem 2012 Dec 24;287(51):42480-94. Epub 2012 Oct 24.

Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.

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http://dx.doi.org/10.1074/jbc.M112.390112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522250PMC
December 2012

Simplification of the genetic code: restricted diversity of genetically encoded amino acids.

Nucleic Acids Res 2012 Nov 21;40(20):10576-84. Epub 2012 Aug 21.

Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Midori-ku, Yokohama-shi, Kanagawa 226-8503, Japan.

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http://dx.doi.org/10.1093/nar/gks786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488234PMC
November 2012

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Zucchini from Drosophila melanogaster.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2012 Nov 30;68(Pt 11):1346-50. Epub 2012 Oct 30.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S1744309112038936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515378PMC
November 2012

Spatial distribution of cytoplasmic domains of the Mg(2+)-transporter MgtE, in a solution lacking Mg(2+), revealed by paramagnetic relaxation enhancement.

Biochim Biophys Acta 2012 Oct 26;1824(10):1129-35. Epub 2012 Jun 26.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1016/j.bbapap.2012.06.008DOI Listing
October 2012

Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex.

Nucleic Acids Res 2012 Oct 5;40(18):9319-28. Epub 2012 Jul 5.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gks660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467058PMC
October 2012

Molecular dynamics simulation of Autotaxin: roles of the nuclease-like domain and the glycan modification.

J Phys Chem B 2012 Oct 24;116(39):11798-808. Epub 2012 Sep 24.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1021/jp303198uDOI Listing
October 2012

Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.

Proc Natl Acad Sci U S A 2012 Oct 1;109(42):16876-81. Epub 2012 Oct 1.

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1073/pnas.1208017109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479499PMC
October 2012

Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation.

EMBO J 2012 Oct 28;31(19):3856-70. Epub 2012 Aug 28.

Laboratory of Molecular Cell Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.

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http://dx.doi.org/10.1038/emboj.2012.241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463848PMC
October 2012

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp1.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2012 Jul 27;68(Pt 7):778-82. Epub 2012 Jun 27.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1107/S1744309112019306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3388920PMC
July 2012

A 3D view of autotaxin.

Trends Pharmacol Sci 2012 Mar 23;33(3):138-45. Epub 2012 Jan 23.

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1016/j.tips.2011.12.004DOI Listing
March 2012

Crystal structure of the channelrhodopsin light-gated cation channel.

Nature 2012 Jan 22;482(7385):369-74. Epub 2012 Jan 22.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/nature10870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160518PMC
January 2012

Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Nov 27;67(Pt 11):1367-70. Epub 2011 Oct 27.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S1744309111031885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212452PMC
November 2011

Structure and function of a membrane component SecDF that enhances protein export.

Nature 2011 May 11;474(7350):235-8. Epub 2011 May 11.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1038/nature09980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697915PMC
May 2011

Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.

Nucleic Acids Res 2011 Mar 23;39(4):1576-85. Epub 2010 Oct 23.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gkq919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045595PMC
March 2011

Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.

Proc Natl Acad Sci U S A 2011 Mar 15;108(10):3912-7. Epub 2011 Feb 15.

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, 113-0032 Tokyo, Japan.

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http://dx.doi.org/10.1073/pnas.1019480108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053990PMC
March 2011

C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).

Nucleic Acids Res 2011 Feb 24;39(3):1034-41. Epub 2010 Sep 24.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1093/nar/gkq845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035459PMC
February 2011

Crystal structure of autotaxin and insight into GPCR activation by lipid mediators.

Nat Struct Mol Biol 2011 Feb 16;18(2):205-12. Epub 2011 Jan 16.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1038/nsmb.1998DOI Listing
February 2011

Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation.

Nucleic Acids Res 2010 Nov 3;38(20):7286-97. Epub 2010 Jul 3.

Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkq605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978374PMC
November 2010

Expanding role of the jumonji C domain as an RNA hydroxylase.

J Biol Chem 2010 Nov 25;285(45):34503-7. Epub 2010 Aug 25.

Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

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http://dx.doi.org/10.1074/jbc.M110.156398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966065PMC
November 2010

Omnipotent role of archaeal elongation factor 1 alpha (EF1α in translational elongation and termination, and quality control of protein synthesis.

Proc Natl Acad Sci U S A 2010 Nov 25;107(45):19242-7. Epub 2010 Oct 25.

Division of Molecular Biology, Department of Basic Medical Science, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1073/pnas.1009599107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984191PMC
November 2010

Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.

Proc Natl Acad Sci U S A 2010 Oct 27;107(41):17575-9. Epub 2010 Sep 27.

Division of Structure Biology, Department of Basic Medical Sciences, The Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1073/pnas.1009598107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955123PMC
October 2010

[Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality].

Seikagaku 2010 Jul;82(7):617-23

Depatment of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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July 2010

Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon.

Biochemistry 2010 Feb;49(5):945-50

RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1021/bi901594wDOI Listing
February 2010

Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis.

EMBO J 2009 Nov 1;28(22):3602-12. Epub 2009 Oct 1.

Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1038/emboj.2009.288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782099PMC
November 2009

Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter.

Structure 2009 Oct 3;17(10):1345-55. Epub 2009 Sep 3.

Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1016/j.str.2009.08.007DOI Listing
October 2009

Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.

Nature 2009 Oct;461(7267):1144-8

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.

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http://dx.doi.org/10.1038/nature08474DOI Listing
October 2009

Structure of a tRNA-dependent kinase essential for selenocysteine decoding.

Proc Natl Acad Sci U S A 2009 Sep 10;106(38):16215-20. Epub 2009 Sep 10.

Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1073/pnas.0908861106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752577PMC
September 2009