Yamagata Atsushi

Profile Information

J-GLOBAL ID: 201801012881554905
researchmap Member ID: B000317459

Research Interests

Research Areas

Life sciences / Structural biochemistry /

Papers

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 …

Nature Communications, 13(1), Dec, 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(1), Nov 23, 2022 Peer-reviewed
Structural basis for activation of DNMT1

Kikuchi Amika, Hiroki Onoda, Kosuke Yamaguchi, Satomi Kori, Shun Matsuzawa, yoshie chiba, Shota Tanimoto, Sae Yoshimi, Hiroki Sato, Atsushi Yamagata …

Nature Communications, 13(1), Nov 21, 2022 Peer-reviewed
Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.

Sakie Katsumura, Nadeem Siddiqui, Michael Rock Goldsmith, Jaime H Cheah, Teppei Fujikawa, Genki Minegishi, Atsushi Yamagata, Yukako Yabuki, Kaoru Kobayashi, Mikako Shirouzu …

Cell metabolism, 34(4) 564-580, Apr 5, 2022 Peer-reviewed
14-3-3 proteins stabilize LGI1-ADAM22 levels to regulate seizure thresholds in mice

Norihiko Yokoi, Yuko Fukata, Kei Okatsu, Atsushi Yamagata, Yan Liu, Makoto Sanbo, Yuri Miyazaki, Teppei Goto, Manabu Abe, Hidetoshi Kassai …

Cell Reports, 37(11) 110107-110107, Dec, 2021
Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice

Tomoyuki Yoshida, Atsushi Yamagata, Ayako Imai, Juhyon Kim, Hironori Izumi, Shogo Nakashima, Tomoko Shiroshima, Asami Maeda, Shiho Iwasawa-Okamoto, Kenji Azechi …

Nature Communications, 12(1), Dec, 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(25) eabf8864-eabf8864, Jun, 2021
LGI1–ADAM22–MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention

Yuko Fukata, Xiumin Chen, Satomi Chiken, Yoko Hirano, Atsushi Yamagata, Hiroki Inahashi, Makoto Sanbo, Hiromi Sano, Teppei Goto, Masumi Hirabayashi …

Proceedings of the National Academy of Sciences, 118(3) e2022580118-e2022580118, Jan 19, 2021 Peer-reviewed
A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.

Ryutaro Shirakawa, Sakurako Goto-Ito, Kota Goto, Shonosuke Wakayama, Haremaru Kubo, Natsumi Sakata, Duc Anh Trinh, Atsushi Yamagata, Yusuke Sato, Hiroshi Masumoto …

The EMBO journal, e104120, Mar 3, 2020 Peer-reviewed
Structural insights into selective interaction between type IIa receptor protein tyrosine phosphatases and Liprin-α.

Maiko Wakita, Atsushi Yamagata, Tomoko Shiroshima, Hironori Izumi, Asami Maeda, Mizuki Sendo, Ayako Imai, Keiko Kubota, Sakurako Goto-Ito, Yusuke Sato …

Nature communications, 11(1) 649-649, Jan 31, 2020 Peer-reviewed
Insights into the mechanisms of epilepsy from structural biology of LGI1-ADAM22.

Atsushi Yamagata, Shuya Fukai

Cellular and molecular life sciences : CMLS, 77(2) 267-274, Jan, 2020 Peer-reviewed
Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.

Yusuke Sato, Hikaru Tsuchiya, Atsushi Yamagata, Kei Okatsu, Keiji Tanaka, Yasushi Saeki, Shuya Fukai

Nature communications, 10(1) 5708-5708, Dec 13, 2019 Peer-reviewed
Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein.

Tomio S Takahashi, Yusuke Sato, Atsushi Yamagata, Sakurako Goto-Ito, Masafumi Saijo, Shuya Fukai

Nucleic acids research, 47(7) 3784-3794, Apr 23, 2019 Peer-reviewed
Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.

Sakurako Goto-Ito, Nobukatsu Morooka, Atsushi Yamagata, Yusuke Sato, Ken Sato, Shuya Fukai

Life science alliance, 2(2), Apr, 2019 Peer-reviewed
Structural insights into leucine-rich repeat-containing synaptic cleft molecules.

Atsushi Yamagata, Shuya Fukai

Current opinion in structural biology, 54 68-77, Feb, 2019 Peer-reviewed
Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168

Tomio S. Takahashi, Yoshihiro Hirade, Aya Toma, Yusuke Sato, Atsushi Yamagata, Sakurako Goto-Ito, Akiko Tomita, Shinichiro Nakada, Shuya Fukai

Nature Communications, 9(1) 170, Dec 1, 2018 Peer-reviewed
Structural basis of trans-synaptic interactions between PTPδ and SALMs for inducing synapse formation

Sakurako Goto-Ito, Atsushi Yamagata, Yusuke Sato, Takeshi Uemura, Tomoko Shiroshima, Asami Maeda, Ayako Imai, Hisashi Mori, Tomoyuki Yoshida, Shuya Fukai

Nature Communications, 9(1) 269, Dec 1, 2018 Peer-reviewed
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 …

Nature Communications, 9(1) 1546, Dec, 2018 Peer-reviewed
Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction.

Atsushi Yamagata, Sakurako Goto-Ito, Yusuke Sato, Tomoko Shiroshima, Asami Maeda, Masahiko Watanabe, Takashi Saitoh, Katsumi Maenaka, Tohru Terada, Tomoyuki Yoshida …

Nature communications, 9(1) 3964-3964, Sep 27, 2018 Peer-reviewed
Structural insights into ubiquitin phosphorylation by PINK1.

Okatsu K, Sato Y, Yamano K, Matsuda N, Negishi L, Takahashi A, Yamagata A, Goto-Ito S, Mishima M, Ito Y …

Scientific reports, 8(1) 10382-10382, Jul, 2018 Peer-reviewed

Misc.

ユビキチン・コード:細胞内の最も難解な暗号を読む USP30によるLys6結合型ユビキチン鎖特異的切断機構の構造的基盤

佐藤裕介, 尾勝圭, 佐伯泰, 山野晃史, 松田憲之, 海保愛, 山形敦史, 伊藤桜子, 石川稔, 橋本祐一 …

生命科学系学会合同年次大会, 2017年度 [4AW13-6], Dec, 2017
遺伝子点変異による精神神経疾患の発症機構解明シナプスオーガナイザー遺伝子点変異導入マウスを用いた神経発達障害発症機構の解明

吉田知之, 山形敦史, 田端彩子, 和泉宏謙, 城島知子, 金主賢, 深田優子, 深田正紀, 高雄啓三, 森寿 …

日本生物学的精神医学会・日本神経精神薬理学会合同年会プログラム・抄録集, 39回・47回 82-82, Sep, 2017
Crystal structure of exonuclease RecJ bound to manganese ion

A Yamagata, Y Kakuta, R Masui, K Fukuyama

BIOPHYSICAL JOURNAL, 82(1) 123A-123A, Jan, 2002

Research Projects

クライオ電顕を用いた鉄錯体輸送体の基質認識と輸送機構の解明

科学研究費助成事業基盤研究(B), 基盤研究(B), 日本学術振興会, Apr, 2022 - Mar, 2025

山形敦史, 寺田透, 難波康祐, 村田佳子
神経変性疾患に関わる凝集体の形成・抑制の in situ 構造生物学

科学研究費助成事業学術変革領域研究(A), 学術変革領域研究(A), 日本学術振興会, Sep, 2021 - Mar, 2023

山形敦史
Structural basis of the novel mechanism to regulate the synapse formation

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B), Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2019 - Mar, 2022

Yamagata Atsushi
X-ray crystallography of molecular complexes regulating vesicular trafficking

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Apr, 2010 - Mar, 2015

FUKAI Shuya, ATSUSHI Yamagata, SATO Yusuke
Structural analyses for yeast Asna-1 ATPase (Get3)

Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, Apr, 2008 - Mar, 2010

ATSUSHI Yamagata
Exocyst複合体の再構成と構造解析

科学研究費助成事業特定領域研究, 特定領域研究, 日本学術振興会, 2008 - 2009

深井周也, 山形敦史, 三村久敏
膜蛋白質のコンフォメーション特異的な結晶化を可能にする抗体断片の開発

科学研究費助成事業特定領域研究, 特定領域研究, 日本学術振興会, 2008 - 2009

三村久敏, 山形敦史, 深井周也
高度好熱菌由来のDNA修復酵素の構造と機能の研究

科学研究費助成事業特別研究員奨励費, 特別研究員奨励費, 日本学術振興会, 2001 - 2002

山形敦史

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