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Citation: Xiaorui Xing, Lei Wang, Zhen Cui, Wangjun Fu, Tao Zheng, Lili Qin, Pingju Ge, Aidong Qian, Nan Wang, Shuai Yuan. Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants [J].VIROLOGICA SINICA, 2022, 37(6) : 938-941.  http://dx.doi.org/10.1016/j.virs.2022.11.003

Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants

  • Highlights
    1 Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift.
    2 T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult.
    3 The overall structures of the closed state S complex from different variants resemble each other.
    4 Mutations in FPPR may affect the overall structure of the trimeric spike protein.

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  • 10.1016j.virs.2022.11.003-ESM.docx
    1. Cai, Y., Zhang, J., Xiao, T., Peng, H., Sterling, S.M., Walsh Jr., R.M., Rawson, S., RitsVolloch, S., Chen, B., 2020. Distinct conformational states of SARS-CoV-2 spike protein. Science 369, 1586–1592.

    2. Cui, Z., Liu, P., Wang, N., Wang, L., Fan, K., Zhu, Q., Wang, K., Chen, R., Feng, R., Jia, Z., Yang, M., Xu, G., Zhu, B., Fu, W., Chu, T., Feng, L., Wang, Y., Pei, X., Yang, P., Xie, X.S., Cao, L., Cao, Y., Wang, X., 2022. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell 185, 860–871.e13.

    3. Harvey, W.T., Carabelli, A.M., Jackson, B., Gupta, R.K., Thomson, E.C., Harrison, E.M., Ludden, C., Reeve, R., Rambaut, A., Consortium, C.-G.U., Peacock, S.J., Robertson, D.L., 2021. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409–424.

    4. Hoffmann, M., Kleine-Weber, H., Pöhlmann, S., 2020. A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells. Mol. Cell 78, 779–784.e775.

    5. Kimura, I., Kosugi, Y., Wu, J., Zahradnik, J., Yamasoba, D., Butlertanaka, E.P., Tanaka, Y.L., Uriu, K., Liu, Y., Morizako, N., Shirakawa, K., Kazuma, Y., Nomura, R., Horisawa, Y., Tokunaga, K., Ueno, T., Takaori-Kondo, A., Schreiber, G., Arase, H., Genotype to Phenotype Japan, C., Motozono, C., Saito, A., Nakagawa, S., Sato, K., 2022. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep. 38, 110218.

    6. Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B., Hastie, K.M., Parker, M.D., Partridge, D.G., Evans, C.M., Freeman, T.M., de Silva, T.I., McDanal, C., Perez, L.G., Tang, H., Moon-Walker, A., Whelan, S.P., LaBranche, C.C., Saphire, E.O., Montefiori, D.C., 2020. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182, 812–827.e819.

    7. Walls, A.C., Tortorici, M.A., Snijder, J., Xiong, X., Bosch, B.J., Rey, F.A., Veesler, D., 2017. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc. Natl. Acad. Sci. U. S. A. 114, 11157–11162.

    8. Zhang, J., Xiao, T., Cai, Y., Chen, B., 2021. Structure of SARS-CoV-2 spike protein. Curr. Opin. Virol. 50, 173–182.

    9. Zhang, L., Jackson, C.B., Mou, H., Ojha, A., Peng, H., Quinlan, B.D., Rangarajan, E.S., Pan, A., Vanderheiden, A., Suthar, M.S., Li, W., Izard, T., Rader, C., Farzan, M., Choe, H., 2020. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat. Commun. 11, 6013.

    10. Zhou, P., Yang, X.L., Wang, X.G., Hu, B., Zhang, L., Zhang, W., Si, H.R., Zhu, Y., Li, B., Huang, C.L., Chen, H.D., Chen, J., Luo, Y., Guo, H., Jiang, R.D., Liu, M.Q., Chen, Y., Shen, X.R., Wang, X., Zheng, X.S., Zhao, K., Chen, Q.J., Deng, F., Liu, L.L., Yan, B., Zhan, F.X., Wang, Y.Y., Xiao, G.F., Shi, Z.L., 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273.

    11. Zhou, T., Tsybovsky, Y., Gorman, J., Rapp, M., Cerutti, G., Chuang, G.Y., Katsamba, P.S., Sampson, J.M., Schön, A., Bimela, J., Boyington, J.C., Nazzari, A., Olia, A.S., Shi, W., Sastry, M., Stephens, T., Stuckey, J., Teng, I.T., Wang, P., Wang, S., Zhang, B., Friesner, R.A., Ho, D.D., Mascola, J.R., Shapiro, L., Kwong, P.D., 2020. Cryo-EM structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-dependent switch to mediate endosomal positioning of receptor-binding domains. Cell Host Microbe 28, 867–879.e865.

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    Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants

      Corresponding author: Aidong Qian, qianaidong0115@163.com
      Corresponding author: Nan Wang, wangnan161@ibp.ac.cn
      Corresponding author: Shuai Yuan, yuanshuai@wh.iov.cn
    • a College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China;
    • b College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China;
    • c CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China;
    • d University of Chinese Academy of Sciences, Beijing, 100101, China;
    • e Acrobiosystems, Beijing, 100101, China;
    • f State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China

    Abstract: Highlights
    1 Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift.
    2 T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult.
    3 The overall structures of the closed state S complex from different variants resemble each other.
    4 Mutations in FPPR may affect the overall structure of the trimeric spike protein.

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