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

Xiaorui Xing; Lei Wang; Zhen Cui; Wangjun Fu; Tao Zheng; Lili Qin; Pingju Ge; Aidong Qian; Nan Wang; Shuai Yuan

doi:10.1016/j.virs.2022.11.003

December 2022

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 .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

Xiaorui Xing ^a,b,c ,
Lei Wang ^c,d ,
Zhen Cui ^c,d ,
Wangjun Fu ^c,d ,
Tao Zheng ^c,d ,
Lili Qin ^e ,
Pingju Ge ^e ,
Aidong Qian ^{a,b
,,} ,
Nan Wang ^{c
,,} ,
Shuai Yuan ^{f
,,}

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

Corresponding author: Aidong Qian, qianaidong0115@163.com
Nan Wang, wangnan161@ibp.ac.cn
Shuai Yuan, yuanshuai@wh.iov.cn
Received Date: 30 June 2022
Accepted Date: 04 November 2022
Available online: 08 November 2022

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.

Electronic Supplementary Material

10.1016j.virs.2022.11.003-ESM.docx
References
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.
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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

Received Date: 30 June 2022

Accepted Date: 04 November 2022

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

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