Publications

Sekine S, Ehara H, Kujirai T, et al.
Structural perspectives on transcription in chromatin
Trends in Cell Biology Thu Aug 17 00:00:00 JST 2023 doi: 10.1016/j.tcb.2023.07.011

Osawa T, Aoki M, Ehara H, et al.
Structures of dengue virus RNA replicase complexes
Molecular Cell Wed Jul 12 00:00:00 JST 2023 doi: 10.1016/j.molcel.2023.06.023

Osumi K, Kujirai T, Ehara H, et al.
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome
Journal of Molecular Biology 435(13), 168130 Sat Jul 01 00:00:00 JST 2023 doi: 10.1016/j.jmb.2023.168130

Kujirai T, Ehara H, Sekine S, Kurumizaka H.
Structural Transition of the Nucleosome during Transcription Elongation
Cells 12(10), 1388 Sun May 14 00:00:00 JST 2023 doi: 10.3390/cells12101388

Ohtomo H, Ito S, McKenzie N.J., et al.
H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation
Journal of Molecular Biology 435(4), 167936 Tue Feb 28 00:00:00 JST 2023 doi: 10.1016/j.jmb.2022.167936

Murayama Y, Ehara H, Aoki M, et al.
Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus
Science Advances 9(6), eade7093 Fri Feb 10 00:00:00 JST 2023 doi: 10.1126/sciadv.ade7093

Hirano R, Ehara H, Kujirai T, et al.
Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1
Nature Communications 13, 7287 Sat Nov 26 00:00:00 JST 2022 doi: 10.1038/s41467-022-35003-z

Inouye S, Sato J, Sahara-Miura Y, et al..
Reverse mutants of the catalytic 19 kDa mutant protein (nanoKAZ/nanoLuc) from Oplophorus luciferase with coelenterazine as preferred substrate
PLOS One Wed Sep 21 00:00:00 JST 2022 doi: 10.1371/journal.pone.0272992

Ehara H, Kujirai T, et al.
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT
Science 377(6611), abp9466 Thu Aug 18 00:00:00 JST 2022 doi: 10.1126/science.abp9466

Fukushima Y, Hatazawa S, Hirai S, et al.
Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones
J Biochem 172(2), 79-88 Fri Apr 29 00:00:00 JST 2022 doi: 10.1093/jb/mvac043

Hosaka T, Nomura T, Kubo M, et al.
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers
PNAS 119(9), e2117433119 Wed Feb 23 00:00:00 JST 2022 doi: 10.1073/pnas.2117433119

Sekine S, Uejima T, Ehara H.
RNA Polymerase-associated Transcription Elongation Factors
RNA Polymerases as Molecular Motors 2nd ed, Chapter 4 Wed Dec 15 00:00:00 JST 2021 doi: 10.1039/9781839160561-00072

Ehara H, Kujirai T, et al.
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science 363(6428), 744-747 Sun Dec 01 00:00:00 JST 2019 doi: 10.1126/science.aav8912

Shimizu H, Saito A, Mikuni J, et al.
Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.
Plos Neglected Tropical Diseases 13(11), e0007894 Fri Nov 01 00:00:00 JST 2019 doi: 10.1371/journal.pntd.0007894

Kujirai T, Ehara H, et al.
Structural basis of the nucleosome transition during RNA polymerase II passage.
Science 362(6414), 595-598 Sat Dec 01 00:00:00 JST 2018 doi: 10.1126/science.aau9904

Shimizu H, Tosaki A, Ohsawa N, et al.
Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion.
J. Biol. Chem. 292, 13428-13440 Fri Dec 01 00:00:00 JST 2017

Ooi WY, Murayama Y, Mekler V, et al.
A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.
Nucleic Acids Research 46(1), 431-441 Fri Dec 01 00:00:00 JST 2017 doi: 10.1093/nar/gkx1162

Ehara H, Yokoyama T, Shigematsu H, et al.
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Science 357(6354), 921-924 Wed Nov 01 00:00:00 JST 2017 doi: 10.1126/science.aan8552

Ehara H, Umehara T, Sekine SI, Yokoyama S.
Crystal structure of RNA polymerase II from Komagataella pastoris.
Biochemical and Biophysical Research Communications 487(2), 230-235 Sat May 27 00:00:00 JST 2017 doi: 10.1016/j.bbrc.2017.04.039

Tomabechi Y, Hosoya T, Ehara H, et al.
Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine.
Biochem. Biophys. Res. Commun. 470, 88-93 Thu Dec 01 00:00:00 JST 2016

Shimizu H, Miyazaki H, Ohsawa N, et al.
Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits.
Scientific Reports 6, 26618 Thu Dec 01 00:00:00 JST 2016 doi: 10.1038/srep26618

Ehara H, Makino M, Kodama K, et al.
Crystal structure of okadaic acid binding protein 2.1: a sponge protein implicated in cytotoxin accumulation.
Chembiochem 16, 1435-1439 Tue Dec 01 00:00:00 JST 2015

Antonopoulos IH, Murayama Y, Warner BA, et al.
Time-resolved Raman and polyacrylamide gel electrophoresis observations of nucleotide incorporation and misincorporation in RNA within a bacterial RNA polymerase crystal.
Biochemistry 54, 652-665 Tue Dec 01 00:00:00 JST 2015

Yanagisawa T, Ishii R, Hikida Y, et al.
A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA ^Cys.
J. Struct. Funct. Genomics. 16, 25-41 Tue Dec 01 00:00:00 JST 2015

Ito T, Masuda I, Yoshida K, et al.
Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc. Natl. Acad. Sci. U.S.A. 112, E4197-205 Tue Dec 01 00:00:00 JST 2015

Itoh Y, Sekine S, Yokoyama S.
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB.
Nucleic Acids Res. 43, 9028-9038 Tue Dec 01 00:00:00 JST 2015

Sekine S, Murayama Y, Svetlov V, et al.
Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations.
Transcription 6(3), 56-60 Tue Dec 01 00:00:00 JST 2015 doi: 10.1080/21541264.2015.1059922

Sekine S, Murayama Y, Svetlov V, et al.
The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.
Molecular Cell 57(3), 408-421 Sun Nov 01 00:00:00 JST 2015 doi: 10.1016/j.molcel.2014.12.014

Itoh Y, Bröcker MJ, Sekine S, et al.
Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.
J. Mol. Biol. 426, 1723-1735 Mon Dec 01 00:00:00 JST 2014

Severinov K, Minakhin L, Sekine S, et al.
Molecular basis of RNA polymerase promoter specificity switch revealed through studies of Thermus bacteriophage transcription regulator.
Bacteriophage 4, e29399 Mon Dec 01 00:00:00 JST 2014

Higo T, Suka N, Ehara H, et al.
Development of a hexahistidine-3×FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris.
J. Struct. Funct. Genomics. 15, 191-199 Mon Dec 01 00:00:00 JST 2014

Naganuma M, Sekine S, Chong YE, et al.
The selective tRNA aminoacylation mechanism based on a single G•U pair.
Nature 510(7506), 507-511 Mon Dec 01 00:00:00 JST 2014 doi: 10.1038/nature13440

Tagami S, Sekine S, Minakhin L, et al.
Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Genes & Development 28(5), 521-531 Sat Nov 01 00:00:00 JST 2014 doi: 10.1101/gad.233916.113

Nakagawa H, Kuratani M, Goto-Ito S, et al.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.
Proteins 81, 1232-1244 Sun Dec 01 00:00:00 JST 2013

Itoh Y, Bröcker MJ, Sekine S, et al.
The decameric SelA tRNA ^Secring structure reveals the mechanism of bacterial selenocysteine formation.
Science 340, 75-78 Sun Dec 01 00:00:00 JST 2013

Itoh Y, Sekine S, Suetsugu S, Yokoyama S.
Tertiary structure of bacterial selenocysteine tRNA.
Nucleic Acids Res. 41, 6729-6738 Sun Dec 01 00:00:00 JST 2013

Itoh Y, Brocker MJ, Sekine S, et al.
Decameric SelA•tRNA^Sec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation.
Science 340(6128), 75-78 Sun Dec 01 00:00:00 JST 2013 doi: 10.1126/science.1229521

Murayama Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase.
Acta Crystallographica. Section F 69, 174-177 Fri Feb 01 00:00:00 JST 2013 doi: 10.1107/S1744309113000055

Itoh Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analysis of bacterial tRNA ^Secin complex with seryl-tRNA synthetase.
Acta Crystallogr. F68, 678-682 Sat Dec 01 00:00:00 JST 2012

Itoh Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analysis of Aquifex aeolicus SelA, a bacterial selenocysteine synthase.
Acta Crystallogr. F68, 1128-1133 Sat Dec 01 00:00:00 JST 2012

Sekine S, Tagami S, Yokoyama S.
Structural basis of transcription by bacterial and eukaryotic RNA polymerases.
Curr. Opin. Struct. Biol. 22, 110-118 Sat Dec 01 00:00:00 JST 2012

Hanawa-Suetsugu K, Kukimoto-Niino M, Mishima-Tsumagari C, et al.
Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc. Natl. Acad. Sci. U. S. A. 109, 3305-3310 Sat Dec 01 00:00:00 JST 2012

Ehara H, Sekine S, Yokoyama S.
Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA Polymerase III.
Protein Sci. 20, 1558-1565 Thu Dec 01 00:00:00 JST 2011

Tagami S, Sekine S, Yokoyama S.
A novel conformation of RNA polymerase sheds light on the mechanism of transcription.
Transcription 2, 162-167 Thu Dec 01 00:00:00 JST 2011

Tagami S, Sekine S, Kumarevel T, et al.
Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1.
Acta Crystallogr. F66, 64-68 Wed Dec 01 00:00:00 JST 2010

Hikida Y, Kuratani M, Bessho Y, et al.
Crystal structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5- methyltransferase.
Acta Crystallogr. D66, 1301-1307 Wed Dec 01 00:00:00 JST 2010

Kuratani M, Hirano M, Goto-Ito S, et al.
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
J. Mol. Biol. 401, 323-333 Wed Dec 01 00:00:00 JST 2010

Chiba S, Itoh Y, Sekine S, Yokoyama S.
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
Mol. Cell 39, 410-420 Wed Dec 01 00:00:00 JST 2010

Tagami S, Sekine S, Kumarevel T, et al.
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
Nature 468(7326), 978-982 Wed Dec 01 00:00:00 JST 2010 doi: 10.1038/nature09573

Itoh Y*, Sekine S*, Matsumoto E, et al.
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
J. Mol. Biol. 385, 1456-1469 Tue Dec 01 00:00:00 JST 2009

Naganuma M, Sekine S, Fukunaga R, Yokoyama S.
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
Proc. Natl. Acad. Sci. U.S.A. 106, 8489-8494 Tue Dec 01 00:00:00 JST 2009

Konno M, Sumida T, Uchikawa E, et al.
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
FEBS J. 276, 4763-4779 Tue Dec 01 00:00:00 JST 2009

Itoh Y, Chiba S, Sekine S, Yokoyama S.
Crystal structure of human selenocysteine tRNA.
Nucleic Acids Res. 37, 6259-6268 Tue Dec 01 00:00:00 JST 2009

Matsumoto E*, Sekine S*, Akasaka R, et al.
Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus.
Acta Crystallogr. F64, 453-458 Mon Dec 01 00:00:00 JST 2008

Itoh Y, Sekine S, Kuroishi C, et al.
Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
RNA Biol. 5, 169-177 Mon Dec 01 00:00:00 JST 2008

Goto-Ito S, Ishii R, Ito T, et al.
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
Acta Crystallogr. D63, 1059-1068 Sat Dec 01 00:00:00 JST 2007

Hiyama TB, Zhao M, Kitago Y, et al.
Structural basis of CoA recognition by the Pyrococcus singledomain CoA-binding proteins.
J. Struct. Funct. Genomics 7, 119-129 Sat Dec 01 00:00:00 JST 2007

Bessho Y, Shibata R, Sekine S, et al.
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Proc. Natl. Acad. Sci. U.S.A. 104, 8293-8298 Sat Dec 01 00:00:00 JST 2007

Shinkai A*, Sekine S*, Urushibata A, et al.
The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodai i contains intrachain and interchain disulfide bonds.
J. Mol. Biol. 372, 1293-1304 Sat Dec 01 00:00:00 JST 2007

Kuratani M, Sakai H, Takahashi M, et al.
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
J. Mol. Biol. 355, 395-408 Fri Dec 01 00:00:00 JST 2006

Iwasaki W, Sekine S, Kuroishi C, et al.
Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.
J. Mol. Biol. 360, 329-342 Fri Dec 01 00:00:00 JST 2006

Sasaki HM, Sekine S, Sengoku T, et al.
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.
Proc. Natl. Acad. Sci. U.S.A. 103, 14744-14749 Fri Dec 01 00:00:00 JST 2006

Sekine S, Shichiri M, Bernier S, et al.
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.
Structure 14, 1791-1799 Fri Dec 01 00:00:00 JST 2006

Kuratani M, Ishii R, Bessho Y, et al.
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.
J. Biol. Chem. 280, 16002-16008 Thu Dec 01 00:00:00 JST 2005

Artsimovitch I, Patlan V, Sekine S, et al.
Structural basis for transcription regulation by alarmone ppGpp.
Cell 117, 299-310 Wed Dec 01 00:00:00 JST 2004

Randau L, Schauer S, Ambrogelly A, et al.
tRNA recognition by glutamyl-tRNA reductase.
J. Biol. Chem. 279, 34931-34937 Wed Dec 01 00:00:00 JST 2004

Hanawa-Suetsugu K, Sekine S, Sakai H, et al.
Crystal structure of elongation factor P from Thermus thermophilus HB8.
Proc. Natl. Acad. Sci. U.S.A. 101, 9595-9600 Wed Dec 01 00:00:00 JST 2004

Vassylyeva MN, Sakai H, Matsuura T, et al.
Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysinebiosynthesis LysX protein from Thermus thermophilus HB8.
Acta Crystallogr. D59, 1651-1652 Mon Dec 01 00:00:00 JST 2003

Sekine S, Nureki O, Dubois DY, et al.
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
EMBO J. 22, 676-688 Mon Dec 01 00:00:00 JST 2003

Fukai S, Nureki O, Sekine S, et al.
Mechanism of molecular interactions for tRNA ^Valrecognition by valyl-tRNA synthetase.
RNA 9, 100-111 Mon Dec 01 00:00:00 JST 2003

Sakai H, Vassylyeva MN, Matsuura T, et al.
Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.
J. Mol. Biol. 332, 729-740 Mon Dec 01 00:00:00 JST 2003

Vassylyeva MN, Lee J, Sekine S, et al.
Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.
Acta Crystallogr. D58, 1497-1500 Sun Dec 01 00:00:00 JST 2002

Vassylyev DG, Sekine S, Laptenko O, et al.
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution.
Nature 417, 712-719 Sun Dec 01 00:00:00 JST 2002

Sekine S, Nureki O, Shimada A, et al.
Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.
Nature Struct. Biol. 8, 203-206 Sat Dec 01 00:00:00 JST 2001

Sekine S, Shimada A, Nureki O, et al.
Crucial role of the HIGH-loop lysine for the catalytic activity of arginyltRNA synthetase.
J. Biol. Chem. 276, 3723-3726 Sat Dec 01 00:00:00 JST 2001

Fukai S, Nureki O, Sekine S, et al.
Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA ^Valand valyl-tRNA synthetase.
Cell 103, 793-803 Fri Dec 01 00:00:00 JST 2000

Sekine S, Nureki O, Tateno M, Yokoyama S.
The identity determinants required for the discrimination between tRNA ^Gluand tRNA ^Aspby glutamyl-tRNA synthetase from Escherichia coli.
Eur. J. Biochem. 261, 354-360 Wed Dec 01 00:00:00 JST 1999

Madore E, Florentz C, Giegé, et al.
Effect of modified nucleotides on Escherichia coli tRNA ^Glustructure and on its aminoacylation by glutamyl-tRNA synthetase. Predominant and distinct roles of the mnm ⁵and s ²modifications of U34.
Eur. J. Biochem. 266, 1128-1135 Wed Dec 01 00:00:00 JST 1999

Sekine S, Nureki O, Sakamoto K, et al.
Major identity determinants in the augmented D helix of tRNA ^Glufrom Escherichia coli.
J. Mol. Biol. 256, 685-700 Sun Dec 01 00:00:00 JST 1996

Nureki O, Vassylyev DG, Katayanagi K, et al.
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science 267, 1958-1965 Fri Dec 01 00:00:00 JST 1995

Tateno M, Nureki O, Sekine S, et al.
A threedimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA.
FEBS Letters 377, 77-81 Fri Dec 01 00:00:00 JST 1995

Shun-ichi Sekine | Laboratory for Transcription Structural Biology