Publication List

（注釈：^* Corresponding authors, ^† First authors）

Protein Functional and Structural Biology Team

Na⁺-mimicking ligands stabilize the inactive state of leukotriene B₄ receptor BLT1.

Hori T, Okuno T, Hirata K, Yamashita K, Kawano Y, Yamamoto M, Hato M, Nakamura M, Shimizu T, Yokomizo T, Miyano M, Yokoyama S.
Nat Chem Biol., 14(3), 262-269 (2018).

Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction.

Matsuda T, Ito T, Takemoto C, Katsura K, Ikeda M, Wakiyama M, Kukimoto-Niino M, Yokoyama S, Kurosawa Y, Shirouzu M,.
PLoS One, 13(2), e0193158 (2018).

Structural Insights into the Altering Function of CRMP2 by Phosphorylation.

Sumi T, Imasaki T, Aoki M, Sakai N, Nitta E, Shirouzu M, Nitta R.
Cell Struct Funct., 43(1), 15-23 (2018).

Identification of pyrrolo[2,3-d]pyrimidines as potent HCK and FLT3-ITD dual inhibitors.

Koda Y, Kikuzato K, Mikuni J, Tanaka A, Yuki H, Honma T, Tomabechi Y, Kukimoto-Niino M, Shirouzu M, Shirai F, Koyama H.
Bioorg Med Chem Lett., 27(22), 4944-4998 (2017).

Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain.

Hasegawa K, Someya Y, Shigematsu H, Kimura-Someya T, Nuemket N, Kumasaka T.
Acta Crystallogr F Struct Biol Commun., 73(Pt 10), 568-573 (2017).

Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation.

Shoji S^*, Hanada K, Ohsawa N, Shirouzu M^*.
Biochem J., 474(18), 3207-3226 (2017).

Structural basis for CRMP2-induced axonal microtubule formation.

Niwa S, Nakamura F, Tomabechi Y, Aoki M, Shigematsu H, Matsumoto T, Yamagata A, Fukai S, Hirokawa N, Goshima Y, Shirouzu M, Nitta R
Sci Rep., 7(1), 10681 (2017).

Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1.

Chase AR, Laudermilch E, Wang J, Shigematsu H, Yokoyama T, Schlieker C.
Mol Biol Cell, 28(21), 2765-2772 (2017).

Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA.

Iwaoka R, Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, Katahira M.
Biomol NMR Assign., 11(2), 265-268 (2017).

Structure of the complete elongation complex of RNA polymerase II with basal factors.

Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI.
Science., 357(6354), 921-924 (2017).

Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA.

Iwaoka R, Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, Katahira M.
Molecules., 22(7), E1207 (2017).

Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion.

Shimizu H, Tosaki A, Ohsawa N, Ishizuka-Katsura Y, Shoji S, Miyazaki H, Oyama F, Terada T, Shirouzu M, Sekine SI, Nukina N, Yokoyama S.
J Biol Chem., 292(32), 13428-13440 (2017).

Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.

Hosaka T, Okazaki M, Kimura-Someya T, Ishizuka-Katsura Y, Ito K, Yokoyama S, Dodo K, Sodeoka M, Shirouzu M.
Protein Sci., 26(9), 1749-1758 (2017).

RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket.

López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR.
Nucleic Acids Res, 45(11), 6945-6959 (2017).

Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.

Yuki H, Kikuzato K, Koda Y, Mikuni J, Tomabechi Y, Kukimoto-Niino M, Tanaka A, Shirai F, Shirouzu M, Koyama H, Honma T.
Bioorg Med Chem., 25(16), 4259-4264 (2017).

A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis.

Katsura K, Matsuda T, Tomabechi Y, Yonemochi M, Hanada K, Ohsawa N, Sakamoto K, Takemoto C^*, Shirouzu M^*.
The Journal of Biochemistry, 162(5), 357-369 (2017).

Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G.

Iwakura N, Yokoyama T, Quaglia F, Mitsuoka K, Mio K, Shigematsu H, Shirouzu M, Kaji A, Kaji H.
PLoS One., 12(5), e0177972 (2017).

Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum.

Nagano-Shoji M, Hamamoto Y, Mizuno Y, Yamada A, Kikuchi M, Shirouzu M, Umehara T, Yoshida M, Nishiyama M, Kosono S.
Mol Microbiol., 104(4), 677-689 (2017).

Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1.

Tajiri H, Uruno T, Shirai T, Takaya D, Matsunaga S, Setoyama D, Watanabe M, Kukimoto-Niino M, Oisaki K, Ushijima M, Sanematsu F, Honma T, Terada T, Oki E, Shirasawa S, Maehara Y, Kang D, Côté JF, Yokoyama S, Kanai M, Fukui Y.
Cell Rep., 19(5), 969-980 (2017).

Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga.

Tamogami J, Kikukawa T, Nara T, Demura M, Kimura-Someya T, Shirouzu M, Yokoyama S, Miyauchi S, Shimono K, Kamo N.
Biophys Physicobiol., 14, 49-55 (2017).

A three-dimensional movie of structural changes in bacteriorhodopsin.

Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, Iwata S.
Science., 354(6319), 1552-1557 (2016).

Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.

Kuwasako K, Nameki N, Tsuda K, Takahashi M, Sato A, Tochio N, Inoue M, Terada T, Kigawa T, Kobayashi N, Shirouzu M, Ito T, Sakamoto T, Wakamatsu K, Güntert P, Takahashi S, Yokoyama S, Muto Y.
Protein Sci., 26(2), 280-291 (2016).

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.

Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E.
Proc Natl Acad Sci U S A., 113(46), 13039-13044 (2016).

SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity.

Muramatsu T, Takemoto C, Kim YT, Wang H, Nishii W, Terada T, Shirouzu M, Yokoyama S.
Proc Natl Acad Sci U S A., 113(46), 12997-13002 (2016).

Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions.

Konomura N, Arai N, Shinohara T, Kobayashi J, Iwasaki W, Ikawa S, Kusano K, Shibata T.
Nucleic Acids Res., 45(1), 337-352 (2016).

Crystal structures of the ATP-binding and ADP-release dwells of the V₁ rotary motor.

Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, Murata T.
Nat Commun., 7, 13235 (2016).

Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A

Wang D, Nitta R, Morikawa M, Yajima H, Inoue S, Shigematsu H, Kikkawa M, Hirokawa N.
Elife, 5, e18101 (2016).

Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin.

Shinoda T, Shinya N, Ito K, Ohsawa N, Terada T, Hirata K, Kawano Y, Yamamoto M, Kimura-Someya T, Yokoyama S^*, Shirouzu M^*.
Sci Rep, 6, 33632 (2016).

Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes.

Terasawa K^†, Tomabechi Y^†, Ikeda M, Ehara H, Kukimoto-Niino M, Wakiyama M, Podyma-Inoue KA, Rajapakshe AR, Watabe T, Shirouzu M, Hara-Yokoyama M.
Biochem Biophys Res Commun, 479(3), 489-495 (2016).

Structural Basis of Cucumisin Protease Activity Regulation by Its Propeptide.

Sotokawauchi A, Kato-Murayama M, Murayama K, Hosaka T, Maeda I, Onjo M, Ohsawa N, Kato DI, Arima K^*, Shirouzu M^*.
J Biochem, 161(1), 45-53 (2016).

TNIK inhibition abrogates colorectal cancer stemness.

Masuda M, Uno Y, Ohbayashi N, Ohata H, Mimata A, Kukimoto-Niino M, Moriyama H, Kashimoto S, Inoue T, Goto N, Okamoto K, Shirouzu M, Sawa M, Yamada T.
Nat Commun, 7, 12586 (2016).

Cell-free methods to produce structurally intact mammalian membrane proteins.

Shinoda T, Shinya N, Ito K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Hirata K, Kawano Y, Yamamoto M, Tomita T, Ishibashi Y, Hirabayashi Y, Kimura-Someya T, Shirouzu M^*, Yokoyama S^*.
Sci Rep, 6, 30442 (2016).

Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility.

Yamagishi M^†, Shigematsu H^†, Yokoyama T, Kikkawa M, Sugawa M, Aoki M, Shirouzu M, Yajima J^*, Nitta R^*.
Structure, 24(8), 1322-1334 (2016).

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.

Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W^*, Shirouzu M^*.
J Biol Chem, 291(34), 17488-17495 (2016).

Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.

Verba KA, Wang RY, Arakawa A, Liu Y, Shirouzu M, Yokoyama S, Agard DA.
Science, 352(6293), 1542-1547 (2016).

Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.

Yip WS, Shigematsu H, Taylor DW, Baserga SJ.
Nucleic Acids Res, 44(18), 8976-8989 (2016).

Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits.

Shimizu H, Miyazaki H, Ohsawa N, Shoji S, Ishizuka-Katsura Y, Tosaki A, Oyama F, Terada T, Sakamoto K, Shirouzu M, Sekine S, Nukina N, Yokoyama S.
Sci Rep, 6, 26618 (2016).

Charge-state-distribution analysis of Bach2 intrinsically disordered heme binding region.

Suenaga T, Watanabe-Matsui M, Uejima T, Shima H, Matsui T, Ikeda-Saito M, Shirouzu M, Igarashi K, Murayama K.
J Biochem, 160(5), 291−298 (2016).

Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding.

Fabbretti A, Schedlbauer A, Brandi L, Kaminishi T, Giuliodori AM, Garofalo R, Ochoa-Lizarralde B, Takemoto C, Yokoyama S, Connell SR, Gualerzi CO, Fucini P.
Proc Natl Acad Sci U S A, 113(16), E2286-2295 (2016).

Binding interactions of the peripheral stalk subunit isoforms from human V-ATPase.

Rahman S, Yamato I, Saijo S, Mizutani K, Takamuku Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Murata T.
Biosci Biotechnol Biochem, 80(5), 878-890 (2016).

Pseudoatomic structure of the tripartite multidrug efflux pump AcrAB-TolC reveals the intermeshing cogwheel-like interaction between AcrA and TolC.

Jeong H, Kim JS, Song S, Shigematsu H, Yokoyama T, Hyun J, Ha NC.
Structure, 24(2), 272-276 (2016).

Statistical modeling and removal of lipid membrane projections for cryo-EM structure determination of reconstituted membrane proteins.

Jensen KH, Brandt SS, Shigematsu H, Sigworth FJ.
J Struct Biol, 194(1), 49-60 (2016).

Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine.

Tomabechi Y, Hosoya T, Ehara H, Sekine S, Shirouzu M, Inouye S.
Biochem Biophys Res Commun, 470(1), 88-93 (2016).

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation

Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S.
Sci Rep, 5, 17204 (2015).

Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA.

Nagano S, Seki E, Lin TY, Shirouzu M, Yokoyama S, Heddle JG.
PLoS One, 10(11), e0142313 (2015).

Structural Basis for the Slow Photocycle and Late Proton Release in Acetabularia Rhodopsin I from the Marine Plant, Acetabularia acetabulum.

Furuse M^†, Tamogami J^†, Hosaka T^†, Kikukawa T, Shinya N, Hato M, Ohsawa N, Kim SY, Jung KH, Demura M, Miyauchi S, Kamo N, Shimono K^*, Kimura-Someya T, Yokoyama S, Shirouzu M^*.
Acta Crystallogr D Biol Crystallogr, 71(Pt 11), 2203-2216 (2015).

Content of intrinsic disorder influences the outcome of cell-free protein synthesis.

Tokmakov AA, Kurotani A, Ikeda M, Terazawa Y, Shirouzu M, Stefanov V, Sakurai T, Yokoyama S.
Sci Rep, 5, 14079 (2015).

A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit.

Yoshida H, Park SY, Oda T, Akiyoshi T, Sato M, Shirouzu M, Tsuda K, Kuwasako K, Unzai S, Muto Y, Urano T, Obayashi E.
Genes Dev., 29(15), 1649-1660 (2015).

Protein stabilization utilizing a redefined codon.

Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N, Haruki M, Kohashi S, Yamagishi K, Murayama K, Tomabechi Y, Itagaki T, Akasaka R, Kawazoe M, Takemoto C, Shirouzu M, Yokoyama S, Sakamoto K.
Sci Rep, 5, 9762 (2015).

X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding.

Morikawa M, Yajima H, Nitta R, Inoue S, Ogura T, Sato C, Hirokawa N.
EMBO J, 34(9), 1270-1286 (2015).

Glycolytic flux controls D-serine synthesis through glyceraldehyde-3-phosphate dehydrogenase in astrocytes.

Suzuki M, Sasabe J, Miyoshi Y, Kuwasako K, Muto Y, Hamase K, Matsuoka M, Imanishi N, Aiso S.
Proc Natl Acad Sci U S A, 112(17), E2217-2224 (2015).

Crystal structures of the human adiponectin receptors.

Tanabe H, Fujii Y, Okada-Iwabu M, Iwabu M, Nakamura Y, Hosaka T, Motoyama K, Ikeda M, Wakiyama M, Terada T, Ohsawa N, Hato M, Ogasawara S, Hino T, Murata T, Iwata S, Hirata K, Kawano Y, Yamamoto M, Kimura-Someya T, Shirouzu M, Yamauchi T, Kadowaki T, Yokoyama S.
Nature, 520(7547), 312-316 (2015).

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.

Tochio N, Umehara T, Nakabayashi K, Yoneyama M, Tsuda K, Shirouzu M, Koshiba S, Watanabe S, Kigawa T, Sasazuki T, Shirasawa S, Yokoyama S.
J Struct Funct Genomics, 16(2), 55-65 (2015).

Preferential recognition of isocitrate dehydrogenase by a rabbit monoclonal antibody (ab124797) against the C-terminal peptide of RANKL.

Terasawa K, Rajapakshe AR, Podyma-Inoue KA, Mishima-Tsumagari C, Yanagishita M, Hara-Yokoyama M.
J Immunol Methods, 420, 1-10 (2015).

Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2.

Tanabe H, Motoyama K, Ikeda M, Wakiyama M, Terada T, Ohsawa N, Hosaka T, Hato M, Fujii Y, Nakamura Y, Ogasawara S, Hino T, Murata T, Iwata S, Okada-Iwabu M, Iwabu M, Hirata K, Kawano Y, Yamamoto M, Kimura-Someya T, Shirouzu M, Yamauchi T, Kadowaki T, Yokoyama S.
J Struct Funct Genomics, 16(1), 11-23 (2015).

Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation.

Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K.
Chembiochem, 16(1), 167-176 (2014).

A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.

Nishii W, Kukimoto-Niino M, Terada T, Shirouzu M, Muramatsu T, Kojima M, Kihara H, Yokoyama S.
Nat Chem Biol, 11(1), 46-51 (2014).

Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase.

Balogun EO, Inaoka DK, Shiba T, Kido Y, Tsuge C, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PA, Kita K, Harada S.
Mol Microbiol, 94(6), 1315-1329 (2014).

Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3.

Tsuda K, Kuwasako K, Nagata T, Takahashi M, Kigawa T, Kobayashi N, Güntert P, Shirouzu M, Yokoyama S, Muto Y.
Proteins, 82(10), 2879-2886 (2014).

The histidine transporter SLC15A4 coordinates mTOR-dependent inflammatory responses and pathogenic antibody production.

Kobayashi T, Shimabukuro-Demoto S, Yoshida-Sugitani R, Furuyama-Tanaka K, Karyu H, Sugiura Y, Shimizu Y, Hosaka T, Goto M, Kato N, Okamura T, Suematsu M, Yokoyama S, Toyama-Sorimachi N.
Immunity, 41(3), 375-388 (2014).

RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing.

Kuwasako K, Takahashi M, Unzai S, Tsuda K, Yoshikawa S, He F, Kobayashi N, Güntert P, Shirouzu M, Ito T, Tanaka A, Yokoyama S, Hagiwara M, Kuroyanagi H, Muto Y.
Nat Struct Mol Biol, 21(9), 778-786 (2014).

Molecular pathogenesis of Spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins

Bin BH, Hojyo S, Hosaka T, Bhin J, Kano H, Miyai T, Ikeda M, Kimura-Someya T, Shirouzu M, Cho EG, Fukue K, Kambe T, Ohashi W, Kim KH, Seo J, Choi DH, Nam YJ, Hwang D, Fukunaka A, Fujitani Y, Yokoyama S, Superti-Furga A, Ikegawa S, Lee TR, Fukada T.
EMBO Mol Med, 6(8), 1028-1042 (2014).

Crystal structures of the S6K1 kinase domain in complexes with inhibitors.

Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S.
J Struct Funct Genomics, 15(3), 153-164 (2014).

Multiple site-specific installations of N^ε-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis.

Yanagisawa T, Takahashi M, Mukai T, Sato S, Wakamori M, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S.
ChemBioChem, 15(12), 1830-1838 (2014).

A new manual dispensing system for in meso membrane protein crystallization with using a stepping motor-based dispenser

Hato M, Hosaka T, Tanabe H, Kitsunai T, Yokoyama S.
J Struct Funct Genomics, 15(3), 165-171 (2014).

Structural Basis for the Specific Recognition of the Major Antigenic Peptide from the Japanese Cedar Pollen Allergen Cry j 1 by HLA-DP5.

Kusano S, Kukimoto-Niino M, Satta Y, Ohsawa N, Uchikubo-Kamo T, Wakiyama M, Ikeda M, Terada T, Yamamoto K, Nishimura Y, Shirouzu M, Sasazuki T, Yokoyama S.
J Mol Biol, 426(17), 3016-3027 (2014).

Allosteric regulation of γ-secretase activity by a phenylimidazole-type γ-secretase modulator.

Takeo K, Tanimura S, Shinoda T, Osawa S, Zahariev IK, Takegami N, Ishizuka-Katsura Y, Shinya N, Takagi-Niidome S, Tominaga A, Ohsawa N, Kimura-Someya T, Shirouzu M, Yokoshima S, Yokoyama S, Fukuyama T, Tomita T, Iwatsubo T.
Proc Natl Acad Sci U S A, 111(29), 10544-10549 (2014).

The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation

Shoji S, Muto Y, Ikeda M, He F, Tsuda K, Ohsawa N, Akasaka R, Terada T, Wakiyama M, Shirouzu M^*, Yokoyama S^*.
FEBS Open Bio, 4, 689-703 (2014).

Crystal structure of tRNA m¹A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.

Kuratani M, Yanagisawa T, Ishii R, Matsuno M, Si SY, Katsura K, Ushikoshi-Nakayama R, Shibata R, Shirouzu M, Bessho Y, Yokoyama S.
J Struct Funct Genomics, 15(3), 173-180 (2014).

Conserved Neutralizing Epitope at Globular Head of Hemagglutinin in H3N2 Influenza Viruses.

Iba Y, Fujii Y, Ohshima N, Sumida T, Kubota-Koketsu R, Ikeda M, Wakiyama M, Shirouzu M, Okada J, Okuno Y, Kurosawa Y, Yokoyama S.
J Virol, 88(13), 7130-7144 (2014).

Structural basis for promoter specificity switching of RNA polymerase by a phage factor.

Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S.
Genes Dev, 28(5), 521-531 (2014).

Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.

Parker LJ, Taruya S, Tsuganezawa K, Ogawa N, Mikuni J, Honda K, Tomabechi Y, Handa N, Shirouzu M, Yokoyama S, Tanaka A.
Acta Crystallogr D Biol Crystallogr, 70(PT 2), 392-404 (2014).

Mutant LV^476-7AA of A-subunit of Enterococcus hirae V₁-ATPase: High affinity of A₃B₃ complex to DF axis and low ATPase activity

Alam J, Yamato I, Arai S, Saijo S, Mizutani K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Kakinuma Y, Murata T.
Springerplus, 2(689), 1-7 (2013).

HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor.

Sakata K, Hara M, Terada T, Watanabe N, Takaya D, Yaguchi S, Matsumoto T, Matsuura T, Shirouzu M, Yokoyama S, Yamaguchi T, Miyazawa K, Aizaki H, Suzuki T, Wakita T, Imoto M, Kojima S.
Sci Rep, 3, 3243 (2013).

A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity.

Okada-Iwabu M, Yamauchi T, Iwabu M, Honma T, Hamagami K, Matsuda K, Yamaguchi M, Tanabe H, Kimura-Someya T, Shirouzu M, Ogata H, Tokuyama K, Ueki K, Nagano T, Tanaka A, Yokoyama S, Kadowaki T.
Nature, 503(7477), 493-499 (2013).

Basic Properties of Rotary Dynamics of the Molecular Motor Enterococcus hirae V₁-ATPase.

Minagawa Y, Ueno H, Hara M, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Yamato I, Muneyuki E, Noji H, Murata T, Iino R.
J Biol Chem, 288(45), 32700-32707 (2013).

Loose Binding of the DF Axis with the A₃B₃ Complex Stimulates the Initial Activity of Enterococcus hirae V₁-ATPase.

Alam MJ, Arai S, Saijo S, Suzuki K, Mizutani K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Kakinuma Y, Yamato I, Murata T.
PLoS One, 8(9), e74291 (2013).

Immune regulatory functions of DOCK family proteins in health and disease.

Nishikimi A, Kukimoto-Niino M, Yokoyama S, Fukui Y.
Exp Cell Res, 319(15), 2343-2349 (2013).

Ectodomain structures of the CGRP and AM receptors.

Kusano S, Yokoyama S.
Curr Protein Pept Sci, 14(5), 375-385 (2013).

Two-Colored Fluorescence Correlation Spectroscopy Screening for LC3-P62 Interaction Inhibitors.

Tsuganezawa K, Shinohara Y, Ogawa N, Tsuboi S, Okada N, Mori M, Yokoyama S, Noda NN, Inagaki F, Ohsumi Y, Tanaka A.
J Biomol Screen, 18(9), 1103-1109 (2013).

High-resolution crystal structure of the catalytic domain of human dual-specificity phosphatase 26

Won EY, Xie Y, Takemoto C, Chen L, Liu ZJ, Wang BC, Lee D, Woo EJ, Park SG, Shirouzu M, Yokoyama S, Kim SJ, Chi SW.
Acta Crystallogr Sect D-Biol Crystallogr, 69(PT6), 1160-1170 (2013).

Biochemical characterization of highly active Trypanosoma brucei gambiense glycerol kinase, a promising drug target.

Balogun EO, Inaoka DK, Shiba T, Kido Y, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PAM, Harada S, Kita K.
J Biochem, 154(1), 77-84 (2013).

Crystal structure of the guanylate kinase domain from discs large homolog 1 (DLG1/SAP97).

Mori S, Tezuka Y, Arakawa A, Handa N, Shirouzu M, Akiyama T, Yokoyama S.
Biochem Biophys Res Commun, 435(3), 334-338 (2013).

A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo

Saito Y, Yuki H, Kuratani M, Hashizume Y, Takagi S, Honma T, Tanaka A, Shirouzu M, Mikuni J, Handa N, Ogahara I, Sone A, Najima Y, Tomabechi Y, Wakiyama M, Uchida N, Tomizawa-Murasawa M, Kaneko A, Tanaka S, Suzuki N, Kajita H, Aoki Y, Ohara O, Shultz LD, Fukami T, Goto T, Taniguchi S, Yokoyama S, Ishikawa F.
Sci Transl Med, 5(181), 181ra52 (2013).

Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.

Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine S, Shigi N, Yokoyama S.
Proteins, 81(7), 1232-1244 (2013).

Aberrant Assembly of RNA Recognition Motif 1 Links to Pathogenic Conversion of TAR DNA-binding Protein of 43 kDa (TDP-43).

Shodai A, Morimura T, Ido A, Uchida T, Ayaki T, Takahashi R, Kitazawa S, Suzuki S, Shirouzu M, Kigawa T, Muto Y, Yokoyama S, Takahashi R, Kitahara R, Ito H, Fujiwara N, Urushitani M.
J Biol Chem, 288(21), 14886-14905 (2013).

Structure of the hypothetical DUF1811-family protein GK0453 from Geobacillus kaustophilus HTA426.

Padmanabhan, B., Nakamura, Y., Antonyuk, SV., Strange, RW., Hasnain, SS., Yokoyama, S., Bessho, Y
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 69(Pt4), 342-345 (2013).

Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CL^pro) from its polyproteins.

Muramatsu T, Kim YT, Nishii W, Terada T, Shirouzu M, Yokoyama S.
FEBS J., 280(9), 2002-2013 (2013).

Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives.

Niwa H, Handa N, Tomabechi Y, Honda K, Toyama M, Ohsawa N, Shirouzu M, Kagechika H, Hirano T, Umehara T, Yokoyama S.
Acta Crystallogr D Biol Crystallogr, 69(Pt4), 595-602 (2013).

Structure of the trypanosome cyanide-insensitive alternative oxidase.

Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, Kita K.
Proc Natl Acad Sci U S A, 110(12), 4580-4585 (2013).

Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8.

Matsumoto A, Shimizu Y, Takemoto C, Ueda T, Uchiumi T, Ito K.
Acta Crystallogr Sect F Struct Biol Cryst Commun., 69(PT 3), 332-335 (2013).

Prediction of ligand-induced structural polymorphism of receptor interaction sites using machine learning.

Takaya D, Sato T, Yuki H, Sasaki S, Tanaka A, Yokoyama S, Honma T.
J Chem Inf Model, 53(3), 704-716 (2013).

Biochemical and biophysical properties of interactions between subunits of the peripheral stalk region of human V-ATPase.

Rahman S, Yamato I, Saijo S, Mizutani K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Murata T.
PLoS One., 8(2), e55704 (2013).

Rotation mechanism of Enterococcus hirae V₁-ATPase based on asymmetric crystal structures.

Arai S, Saijo S, Suzuki K, Mizutani K, Kakinuma Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Yamato I, Murata T.
Nature, 493(7434), 703-707 (2013).

¹H, ¹³C, and ¹⁵N resonance assignments of the dsRBDs of mouse RNA helicase A.

Nagata T, Tsuda K, Kobayashi N, Güntert P, Yokoyama S, Muto Y.
Biomol NMR Assign, 7(1), 69-72 (2012).

Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.

Yoshikawa S, Kukimoto-Niino M, Parker L, Handa N, Terada T, Fujimoto T, Terazawa Y, Wakiyama M, Sato M, Sano S, Kobayashi T, Tanaka T, Chen L, Liu ZJ, Wang BC, Shirouzu M, Kawa S, Semba K, Yamamoto T, Yokoyama S.
Oncogene, 32(1), 27-38 (2012).