# Equally contributed first authors
* Corresponding author(s)

A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis
Kenjyo Miyauchi#, Satoshi Kimura#, Naho Akiyama#, Kazuki Inoue, Kensuke Ishiguro, Thien-Son Vu, Veerasak Srisuknimit, Kenta Koyama, Gosuke Hayashi, Akiko Soma, Asuteka Nagao, Mikako Shirouzu, Akimitsu Okamoto, Matthew K. Waldor*, Tsutomu Suzuki* Nature Chemical Biology (2024)

Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex
Tatsuo Yanagisawa#, Yuko Murayama#, Haruhiko Ehara, Mie Goto, Mari Aoki, Shun-ichi Sekine* Nature Communications 15, 7854 (2024)

E22G Aβ40 fibril structure and kinetics illuminate how Aβ40 rather than Aβ42 triggers familial Alzheimer’s
Mohammad Jafar Tehrani#, Isamu Matsuda#, Atsushi Yamagata, Yu Kodama, Tatsuya Matsunaga, Mayuko Sato, Kiminori Toyooka, Dan McElheny, Naohiro Kobayashi, Mikako Shirouzu, Yoshitaka Ishii*　Nature Communications 15, 7045 (2024)

RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state
Mutsuko Kukimoto-Niino*, Kazushige Katsura, Yoshiko Ishizuka-Katsura, Chiemi Mishima-Tsumagari, Mayumi Yonemochi, Mio Inoue, Reiko Nakagawa, Rahul Kaushik, Kam Y.J. Zhang, Mikako Shirouzu*　Journal of Biological Chemistory 300, 107459 (2024)

Structural and dynamic insights into the activation of the μ-opioid receptor by an allosteric modulator
Shun Kaneko, Shunsuke Imai*, Tomomi Uchikubo-Kamo, Tamao Hisano, Nobuaki Asao, Mikako Shirouzu, Ichio Shimada*　Nature Communications 15, 3544 (2024)

Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A
Atsushi Yamagata*, Kaori Ito, Takehiro Suzuki, Naoshi Dohmae, Tohru Terada, Mikako Shirouzu　Nature Communications 15, 3027 (2024)

Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography revealing binding sites for human monoclonal antibodies
Tomomi Kimura-Someya*, Kazushige Katsura, Miyuki Kato-Murayama, Toshiaki Hosaka, Tomomi Uchikubo-Kamo, Kentaro Ihara, Kazuharu Hanada, Shin Sato, Kazutaka Murayama, Michiyo Kataoka, Mikako Shirouzu*, Yuichi Someya* Journal of Virology 98, e00197-24 (2024)

Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine
Naho Akiyama, Kensuke Ishiguro, Takeshi Yokoyama, Kenjyo Miyauchi, Asuteka Nagao, Mikako Shirouzu, Tsutomu Suzuki*　Nature Structual & Molecular Biology 31, 817–825 (2024)

Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1
Mayuki Tanaka#, Takeshi Yokoyama#, Hironori Saito#, Madoka Nishimoto, Kengo Tsuda, Naoyuki Sotta, Hideki Shigematsu, Mikako Shirouzu, Shintaro Iwasaki*, Takuhiro Ito* & Toru Fujiwara*　Nature Chemical Biology 20, 605–614 (2024)

ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes
Heeyoun Bunch*, Deukyeong Kim, Masahiro Naganuma, Reiko Nakagawa, Anh Cong, Jaehyeon Jeong, Haruhiko Ehara, Hongha Vu, Jeong Ho Chang, Matthew J Schellenberg, Shun-Ichi Sekine　Nature Communications 14, 8341 (2023)

Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth
Xuewei Zhao#, Ding Ma#, Kensuke Ishiguro#, Hironori Saito, Shinichiro Akichika, Ikuya Matsuzawa, Mari Mito, Toru Irie, Kota Ishibashi, Kimi Wakabayashi, Yuriko Sakaguchi, Takeshi Yokoyama, Yuichiro Mishima, Mikako Shirouzu, Shintaro Iwasaki, Takeo Suzuki*, Tsutomu Suzuki*　Cell 186, 5527-5535 (2023)

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor2
Jae-Hyun Park#, Kouki Kawakami#, Naito Ishimoto, Tatsuya Ikuta, Mio Ohki, Toru Ekimoto, Mitsunori Ikeguchi, Dong-Sun Lee, Young-Ho Lee, Jeremy R. H. Tame, Asuka Inoue* & Sam-Yong Park*　Nature Communications 14, 7150 (2023)

Structures of dengue virus RNA replicase complexes
Takuo Osawa, Mari Aoki, Haruhiko Ehara, Shun-ichi Sekine*　Molecular Cell 83, 2781-2791 (2023)

Epigenetic mechanisms to propagate histone acetylation by p300/CBP
Masaki Kikuchi, Satoshi Morita, Masatoshi Wakamori, Shin Sato, Tomomi Uchikubo-Kamo, Takehiro Suzuki, Naoshi Dohmae, Mikako Shirouzu, Takashi Umehara* Nature Communications 14, 4103 (2023)

Structural basis of CXC chemokine receptor 1 ligand binding and activation
Naito Ishimoto#, Jae-Hyun Park#, Kouki Kawakami, Michiko Tajiri, Kenji Mizutani, Satoko Akashi, Jeremy R H Tame, Asuka Inoue, Sam-Yong Park* Nature Communications 14, 4107 (2023)

Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents
Masaru Takeshita*, Hidehiro Fukuyama, Katsuhiko Kamada, Takehisa Matsumoto, Chieko Makino-Okamura, Qingshun Lin, Machie Sakuma, Eiki Kawahara, Isato Yamazaki, Tomomi Uchikubo-Kamo, Yuri Tomabechi, Kazuharu Hanada, Tamao Hisano, Saya Moriyama, Yoshimasa Takahashi, Mutsumi Ito, Masaki Imai, Tadashi Maemura, Yuri Furusawa, Seiya Yamayoshi, Yoshihiro Kawaoka, Mikako Shirouzu, Makoto Ishii, Hideyuki Saya, Yasushi Kondo, Yuko Kaneko, Katsuya Suzuki, Koichi Fukunaga, Tsutomu Takeuchi, the Keio Donner Project　iScience 26, 106955 (2023)

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus
Yuko Murayama, Haruhiko Ehara, Mari Aoki, Mie Goto, Takeshi Yokoyama, Shun-ichi Sekine* Science Advances eade7093 (2023)

Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus
Laura Bracun, Atsushi Yamagata, Bern M Christianson, Mikako Shirouzu, Lu-Ning Liu*　Structure 31, 318-328 (2023)

Potent SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models
Masaru Takeshita*, Hidehiro Fukuyama, Katsuhiko Kamada, Takehisa Matsumoto, Chieko Makino-Okamura, Tomomi Uchikubo-Kamo, Yuri Tomabechi, Kazuharu Hanada, Saya Moriyama, Yoshimasa Takahashi, Hirohito Ishigaki, Misako Nakayama, Cong Thanh Nguyen, Yoshinori Kitagawa, Yasushi Itoh, Masaki Imai, Tadashi Maemura, Yuri Furusawa, Hiroshi Ueki, Kiyoko Iwatsuki-Horimoto, Mutsumi Ito, Seiya Yamayoshi, Yoshihiro Kawaoka, Mikako Shirouzu, Makoto Ishii, Hideyuki Saya, Yasushi Kondo, Yuko Kaneko, Katsuya Suzuki, Koichi Fukunaga, Tsutomu Takeuchi iScience 25, 105596 (2022)

Uptake mechanism of iron-phytosiderophore from the soil based on the structure of Yellow Stripe transporter
Atsushi Yamagata*, Yoshiko Murata, Kosuke Namba, Tohru Terada, Shuya Fukai, Mikako Shirouzu Nature Communications 13, 7180 (2022)

Structural basis for activation of DNMT1
Amika Kikuchi#, Hiroki Onoda#, Kosuke Yamaguchi, Satomi Kori, Shun Matsuzawa, Yoshie Chiba, Shota Tanimoto, Sae Yoshimi, Hiroki Sato, Atsushi Yamagata, Mikako Shirouzu, Naruhiko Adachi, Jafar Sharif, Haruhiko Koseki, Atsuya Nishiyama, Makoto Nakanishi, Pierre-Antoine Defossez, Kyohei Arita* Nature Communications 13, 7130 (2022)

Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT
Haruhiko Ehara#, Tomoya Kujirai#, Mikako Shirouzu, Hitoshi Kurumizaka*, Shun-ichi Sekine* Science 377 eabp9466 (2022)

METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance
Eriko Matsuura-Suzuki# , Tadahiro Shimazu#*, Mari Takahashi, Kaoru Kotoshiba, Takehiro Suzuki, Kazuhiro Kashiwagi, Yoshihiro Sohtome, Mai Akakabe, Mikiko Sodeoka, Naoshi Dohmae, Takuhiro Ito*, Yoichi Shinkai*, Shintaro Iwasaki* eLife 11, e72780 (2022)

Structural insights into the HBV receptor and bile acid transporter NTCP
Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi Nomura, So Iwata, Koichi Watashi, Jeremy R. H. Tame, Tomohiro Nishizawa, Weontae Lee*, Sam-Yong Park* Nature 606, 1027–1031 (2022)

Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex
Peng Cao#, Laura Bracun#, Atsushi Yamagata#, Bern M Christianson, Tatsuki Negami, Baohua Zou, Tohru Terada, Daniel P Canniffe, Mikako Shirouzu*, Mei Li*, Lu-Ning Liu* Nature Communications 3, 1977 (2022)

Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system
Yoshiko Nakagawa, Howard C-H Shen, Yusuke Komi, Shinju Sugiyama, Takaaki Kurinomaru, Yuri Tomabechi, Elena Krayukhina, Kenji Okamoto, Takeshi Yokoyama, Mikako Shirouzu, Susumu Uchiyama, Megumi Inaba, Tatsuya Niwa, Yasushi Sako, Hideki Taguchi*, Motomasa Tanaka* Nature Chemical Biology 18, 321–331 (2022)

Chimeric mutants of staphylococcal hemolysin, which act as both one-component and two-component hemolysin, created by grafting the stem domain
Nouran Ghanem, Natsuki Kanagami, Takashi Matsui, Kein Takeda, Jun Kaneko, Yasuyuki Shiraishi, Christian A Choe, Tomomi Uchikubo-Kamo, Mikako Shirouzu, Tsubasa Hashimoto, Tomohisa Ogawa, Tomoaki Matsuura, Po-Ssu Huang, Takeshi Yokoyama, Yoshikazu Tanaka* The FEBS Journal 289, 3505-3520 (2022)

eIF2B-capturing viral protein NSs suppresses the integrated stress response
Kazuhiro Kashiwagi#, Yuichi Shichino#, Tatsuya Osaki#, Ayako Sakamoto, Madoka Nishimoto, Mari Takahashi, Mari Mito, Friedemann Weber, Yoshiho Ikeuchi*, Shintaro Iwasaki*, Takuhiro Ito* Nature Communications 12, 7102 (2021)

Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex
Mutsuko Kukimoto-Niino, Kazushige Katsura, Rahul Kaushik, Haruhiko Ehara, Takeshi Yokoyama, Tomomi Uchikubo-Kamo, Reiko Nakagawa, Chiemi Mishima-Tsumagari, Mayumi Yonemochi, Mariko Ikeda, Kazuharu Hanada, Kam Y. J. Zhang, Mikako Shirouzu* Science Advances 7, eabg3147 (2021)

Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution
Laura Bracun#, Atsushi Yamagata#, Bern M Christianson, Tohru Terada, Daniel P Canniffe, Mikako Shirouzu, Lu-Ning Liu* Science Advances 7, eabf8864 (2021)

Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope
Koki Makabe, Takeshi Yokoyama, Shiro Uehara, Tomomi Uchikubo-Kamo, Mikako Shirouzu, Kouki Kimura, Kouhei Tsumoto, Ryutaro Asano, Yoshikazu Tanaka, Izumi Kumagai* Scientific Reports 11, 5790 (2021)

GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation
Rie Ayukawa#, Seigo Iwata#, Hiroshi Imai#, Shinji Kamimura, Masahito Hayashi, Kien Xuan Ngo, Itsushi Minoura, Seiichi Uchimura, Tsukasa Makino, Mikako Shirouzu, Hideki Shigematsu, Ken Sekimoto*, Benoît Gigant*, Etsuko Muto* The Journal of Cell Biology 220, e202007033 (2021)

ISRIB blunts the integrated stress response by allosterically antagonising the inhibitory effect of phosphorylated eIF2 on eIF2B
Alisa F. Zyryanova#, Kazuhiro Kashiwagi#, Claudia Rato, Heather P. Harding, Ana Crespillo-Casado, Luke A. Perera, Ayako Sakamoto, Madoka Nishimoto, Mayumi Yonemochi, Mikako Shirouzu, Takuhiro Ito*, David Ron* Molecular Cell 81, 88-103 (2021)

Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Ryoki Nakamura#, Tomohiro Numata#, Go Kasuya#*, Takeshi Yokoyama, Tomohiro Nishizawa, Tsukasa Kusakizako, Takafumi Kato, Tatsuya Hagino, Naoshi Dohmae, Masato Inoue, Kengo Watanabe, Hidenori Ichijo, Masahide Kikkawa, Mikako Shirouzu, Thomas J Jentsch, Ryuichiro Ishitani, Yasunobu Okada*, Osamu Nureki*　Communications Biology 3, 240 (2020)

Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc
Yongchan Lee, Pattama Wiriyasermkul, Chunhuan Jin, Lili Quan, Ryuichi Ohgaki, Suguru Okuda, Tsukasa Kusakizako, Tomohiro Nishizawa, Kazumasa Oda, Ryuichiro Ishitani, Takeshi Yokoyama, Takanori Nakane, Mikako Shirouzu, Hitoshi Endou, Shushi Nagamori, Yoshikatsu Kanai, Osamu Nureki*　Nature Structural & Molecular Biology 26, 510–517 (2019)

HCV IRES captures an actively translating 80S ribosome
Takeshi Yokoyama#, Kodai Machida#, Wakana Iwasaki#, Tomoaki Shigeta, Madoka Nishimoto, Mari Takahashi, Ayako Sakamoto, Mayumi Yonemochi, Yoshie Harada, Hideki Shigematsu, Mikako Shirouzu, Hisashi Tadakuma*, Hiroaki Imataka*, Takuhiro Ito*　Molecular Cell 74, 1205–1214 (2019)

Structural Basis for eIF2B Inhibition in Integrated Stress Response
Kazuhiro Kashiwagi, Takeshi Yokoyama, Madoka Nishimoto, Mari Takahashi, Ayako Sakamoto, Mayumi Yonemochi, Mikako Shirouzu, Takuhiro Ito*　Science 364, 95-499 (2019)　

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors
Haruhiko Ehara#, Tomoya Kujirai#, Yuka Fujino, Mikako Shirouzu, Hitoshi Kurumizaka*, Shun-ichi Sekine* Science 363,744-747 (2019)

Metastable asymmetrical structure of a shaftless V1 motor
Shintaro Maruyama#, Kano Suzuki#, Motonori Imamura, Hikaru Sasaki, Hideyuki Matsunami, Kenji Mizutani, Yasuko Saito, Fabiana L Imai, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Takayuki Uchihashi, Toshio Ando, Ichiro Yamato, Takeshi Murata* Science Advances 5,eaau8149(2019)

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport
Tomohiro Shima#, Manatsu Morikawa#, Junichi Kaneshiro, Taketoshi Kambara, Shinji Kamimura, Toshiki Yagi, Hiroyuki Iwamoto, Sotaro Uemura, Hideki Shigematsu, Mikako Shirouzu, Taro Ichimura, Tomonobu M Watanabe, Ryo Nitta, Yasushi Okada*, Nobutaka Hirokawa* The Journal of Cell Biology 217, 4164-4183 (2018)

Structural basis of the nucleosome transition during RNA polymerase II passage
Tomoya Kujirai#, Haruhiko Ehara#, Yuka Fujino, Mikako Shirouzu, Shun-Ichi Sekine*, Hitoshi Kurumizaka* Science 362, 595-598 (2018)

Structural insight into microtubule stabilization and kinesin inhibition by Tau-family MAPs
Hideki Shigematsu#, Tsuyoshi Imasaki#, Chihiro Doki, Takuya Sumi, Mari Aoki, Tomomi Uchikubo-Kamo, Ayako Sakamoto, Kiyotaka Tokuraku, Mikako Shirouzu, Ryo Nitta* The Journal of Cell Biology 217, 4155-4164 (2018)

Cryo-EM structures of the human volume-regulated anion channel LRRC8
Go Kasuya#, Takanori Nakane#, Takeshi Yokoyama#, Yanyan Jia, Masato Inoue, Kengo Watanabe, Ryoki Nakamura, Tomohiro Nishizawa, Tsukasa Kusakizako, Akihisa Tsutsumi, Haruaki Yanagisawa, Naoshi Dohmae, Motoyuki Hattori, Hidenori Ichijo, Zhiqiang Yan, Masahide Kikkawa, Mikako Shirouzu, Ryuichiro Ishitani*, Osamu Nureki* Nature Structural & Molecular Biology 25, 797-804 (2018)

Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22
Atsushi Yamagata#, Yuri Miyazaki#, Norihiko Yokoi, Hideki Shigematsu, Yusuke Sato, Sakurako Goto-Ito, Asami Maeda, Teppei Goto, Makoto Sanbo, Masumi Hirabayashi, Mikako Shirouzu, Yuko Fukata, Masaki Fukata*, Shuya Fukai* Nature Communications 9 1546 (2018)

Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1
Anna R Chase, Ethan Laudermilch, Jimin Wang, Hideki Shigematsu, Takeshi Yokoyama, Christian Schlieker* Molecular Biology of the Cell 28 2765-2772 (2017)

Structural basis for CRMP2-induced axonal microtubule formation
Shinsuke Niwa, Fumio Nakamura, Yuri Tomabechi, Mari Aoki, Hideki Shigematsu, Takashi Matsumoto, Atsushi Yamagata, Shuya Fukai, Nobutaka Hirokawa, Yoshio Goshima, Mikako Shirouzu, Ryo Nitta* Scientific Reports　7, 10681 (2017)

Structure of the complete elongation complex of RNA polymerase II with basal factors
Haruhiko Ehara, Takeshi Yokoyama, Hideki Shigematsu, Shigeyuki Yokoyama, Mikako Shirouzu, Shun-ichi Sekine* Science 357, 921-924 (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
Nobuhiro Iwakura, Takeshi Yokoyama, Fabio Quaglia, Kaoru Mitsuoka, Kazuhiro Mio, Hideki Shigematsu, Mikako Shirouzu, Akira Kaji*, Hideko Kaji* PLoS One 12, e0177972 (2017)