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Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Shun-ichi Sekine | Laboratory for Transcription Structural Biology


Sekine S, Ehara H, Kujirai T, et al.
Structural perspectives on transcription in chromatin
Trends in Cell Biology (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (2013)

Itoh Y, Bröcker MJ, Sekine S, et al.
The decameric SelA tRNA Sec ring structure reveals the mechanism of bacterial selenocysteine formation.
Science 340, 75-78 (2013)

Itoh Y, Sekine S, Suetsugu S, Yokoyama S.
Tertiary structure of bacterial selenocysteine tRNA.
Nucleic Acids Res. 41, 6729-6738 (2013)

Itoh Y, Brocker MJ, Sekine S, et al.
Decameric SelA•tRNASec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation.
Science 340(6128), 75-78 (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 (2013) doi: 10.1107/S1744309113000055

Itoh Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analysis of bacterial tRNA Sec in complex with seryl-tRNA synthetase.
Acta Crystallogr. F68, 678-682 (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 (2012)

Sekine S, Tagami S, Yokoyama S.
Structural basis of transcription by bacterial and eukaryotic RNA polymerases.
Curr. Opin. Struct. Biol. 22, 110-118 (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 (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 (2011)

Tagami S, Sekine S, Yokoyama S.
A novel conformation of RNA polymerase sheds light on the mechanism of transcription.
Transcription 2, 162-167 (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 (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 (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 (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 (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 (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 (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 (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 (2009)

Itoh Y, Chiba S, Sekine S, Yokoyama S.
Crystal structure of human selenocysteine tRNA.
Nucleic Acids Res. 37, 6259-6268 (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 (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 (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 (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 (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 (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 (2007)

Kuratani M, Sakai H, Takahashi M, et al.
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
J. Mol. Biol. 355, 395-408 (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 (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 (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 (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 (2005)

Artsimovitch I, Patlan V, Sekine S, et al.
Structural basis for transcription regulation by alarmone ppGpp.
Cell 117, 299-310 (2004)

Randau L, Schauer S, Ambrogelly A, et al.
tRNA recognition by glutamyl-tRNA reductase.
J. Biol. Chem. 279, 34931-34937 (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 (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 (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 (2003)

Fukai S, Nureki O, Sekine S, et al.
Mechanism of molecular interactions for tRNA Val recognition by valyl-tRNA synthetase.
RNA 9, 100-111 (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 (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 (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 (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 (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 (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 Val and valyl-tRNA synthetase.
Cell 103, 793-803 (2000)

Sekine S, Nureki O, Tateno M, Yokoyama S.
The identity determinants required for the discrimination between tRNA Glu and tRNA Asp by glutamyl-tRNA synthetase from Escherichia coli.
Eur. J. Biochem. 261, 354-360 (1999)

Madore E, Florentz C, Giegé, et al.
Effect of modified nucleotides on Escherichia coli tRNA Glu structure and on its aminoacylation by glutamyl-tRNA synthetase. Predominant and distinct roles of the mnm 5 and s 2 modifications of U34.
Eur. J. Biochem. 266, 1128-1135 (1999)

Sekine S, Nureki O, Sakamoto K, et al.
Major identity determinants in the augmented D helix of tRNA Glu from Escherichia coli.
J. Mol. Biol. 256, 685-700 (1996)

Nureki O, Vassylyev DG, Katayanagi K, et al.
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science 267, 1958-1965 (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 (1995)

* denotes equal contribution.