Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein

Linhua Tai; Guoliang Zhu; Minnan Yang; Lei Cao; Xiaorui Xing; Guoliang Yin; Chun Chan; Chengfeng Qin; Zihe Rao; Xiangxi Wang; Fei Sun; Yun Zhu

doi:10.1073/pnas.2112703118

Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein

Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2112703118. doi: 10.1073/pnas.2112703118.

Authors

Linhua Tai^{1

2}, Guoliang Zhu^{1

2}, Minnan Yang¹, Lei Cao¹, Xiaorui Xing¹, Guoliang Yin^{1

2}, Chun Chan³, Chengfeng Qin⁴, Zihe Rao¹, Xiangxi Wang^{5

6}, Fei Sun^{5

2

7

8}, Yun Zhu⁵

Affiliations

¹ National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
² School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
³ Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210.
⁴ State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
⁵ National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; xiangxi@ibp.ac.cn feisun@ibp.ac.cn zhuyun@ibp.ac.cn.
⁶ Department for Disease Control and Prevention, Guangzhou Laboratory, Guangzhou 510320, China.
⁷ Department of Biomedical Device, Bioland Laboratory, Guangzhou 510005, China.
⁸ Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Abstract

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates membrane fusion to allow entry of the viral genome into host cells. To understand its detailed entry mechanism and develop a specific entry inhibitor, in situ structural information on the SARS-CoV-2 spike protein in different states is urgent. Here, by using cryo-electron tomography, we observed both prefusion and postfusion spikes in β-propiolactone-inactivated SARS-CoV-2 virions and solved the in situ structure of the postfusion spike at nanometer resolution. Compared to previous reports, the six-helix bundle fusion core, the glycosylation sites, and the location of the transmembrane domain were clearly resolved. We observed oligomerization patterns of the spikes on the viral membrane, likely suggesting a mechanism of fusion pore formation.

Keywords: SARS-CoV-2; cryo-electron tomography; postfusion state; spike protein; subtomogram analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Motifs
Animals
Chlorocebus aethiops
Cryoelectron Microscopy
Electron Microscope Tomography
Glycosylation
Protein Domains
Protein Multimerization
SARS-CoV-2 / ultrastructure*
Spike Glycoprotein, Coronavirus / chemistry*
Spike Glycoprotein, Coronavirus / metabolism
Vero Cells

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2