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Structure of SARS-CoV-2 membrane protein essential for virus assembly

Author

Listed:
  • Zhikuan Zhang

    (The University of Tokyo)

  • Norimichi Nomura

    (Kyoto University)

  • Yukiko Muramoto

    (Kyoto University
    Kyoto University
    CREST, Japan Science and Technology Agency)

  • Toru Ekimoto

    (Yokohama City University)

  • Tomoko Uemura

    (Kyoto University)

  • Kehong Liu

    (Kyoto University)

  • Moeko Yui

    (The University of Tokyo)

  • Nozomu Kono

    (The University of Tokyo)

  • Junken Aoki

    (The University of Tokyo)

  • Mitsunori Ikeguchi

    (Yokohama City University
    Center for Computational Science, RIKEN)

  • Takeshi Noda

    (Kyoto University
    Kyoto University
    CREST, Japan Science and Technology Agency)

  • So Iwata

    (Kyoto University
    RIKEN SPring-8 Center, Kouto)

  • Umeharu Ohto

    (The University of Tokyo)

  • Toshiyuki Shimizu

    (The University of Tokyo)

Abstract

The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein.

Suggested Citation

  • Zhikuan Zhang & Norimichi Nomura & Yukiko Muramoto & Toru Ekimoto & Tomoko Uemura & Kehong Liu & Moeko Yui & Nozomu Kono & Junken Aoki & Mitsunori Ikeguchi & Takeshi Noda & So Iwata & Umeharu Ohto & T, 2022. "Structure of SARS-CoV-2 membrane protein essential for virus assembly," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32019-3
    DOI: 10.1038/s41467-022-32019-3
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    References listed on IDEAS

    as
    1. Shan Lu & Qiaozhen Ye & Digvijay Singh & Yong Cao & Jolene K. Diedrich & John R. Yates & Elizabeth Villa & Don W. Cleveland & Kevin D. Corbett, 2021. "The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Peng Zhou & Xing-Lou Yang & Xian-Guang Wang & Ben Hu & Lei Zhang & Wei Zhang & Hao-Rui Si & Yan Zhu & Bei Li & Chao-Lin Huang & Hui-Dong Chen & Jing Chen & Yun Luo & Hua Guo & Ren-Di Jiang & Mei-Qin L, 2020. "Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin," Nature, Nature, vol. 588(7836), pages 6-6, December.
    3. Yuki Shiimura & Shoichiro Horita & Akie Hamamoto & Hidetsugu Asada & Kunio Hirata & Misuzu Tanaka & Kenji Mori & Tomoko Uemura & Takuya Kobayashi & So Iwata & Masayasu Kojima, 2020. "Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    4. Peng Zhou & Xing-Lou Yang & Xian-Guang Wang & Ben Hu & Lei Zhang & Wei Zhang & Hao-Rui Si & Yan Zhu & Bei Li & Chao-Lin Huang & Hui-Dong Chen & Jing Chen & Yun Luo & Hua Guo & Ren-Di Jiang & Mei-Qin L, 2020. "A pneumonia outbreak associated with a new coronavirus of probable bat origin," Nature, Nature, vol. 579(7798), pages 270-273, March.
    5. Takahiro Muraoka & Daiki Noguchi & Rinshi S. Kasai & Kohei Sato & Ryo Sasaki & Kazuhito V. Tabata & Toru Ekimoto & Mitsunori Ikeguchi & Kiyoto Kamagata & Norihisa Hoshino & Hiroyuki Noji & Tomoyuki Ak, 2020. "A synthetic ion channel with anisotropic ligand response," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
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    1. Shengjun Wang & Wei Ran & Lingyu Sun & Qingchi Fan & Yuanqi Zhao & Bowen Wang & Jinghong Yang & Yuqi He & Ying Wu & Yuanyuan Wang & Luoyi Chen & Arpaporn Chuchuay & Yuyu You & Xinhai Zhu & Xiaojuan Wa, 2024. "Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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