Structural and functional mechanism of SARS-CoV-2 cell entry

The novel coronavirus SARS-CoV-2 emerged as a human pathogen in China at the end of 2019 and has since spread across the globe. Understanding the structure and function of this virus is essential to target vaccines and therapies to tackle the COVID-19 disease. 


Overview


SARS-CoV-2 virus

Rapid analysis of the viral pathogen at the beginning of this pandemic revealed that it belongs to the B beta-CoV lineage1,2. Coronaviruses are enveloped, single-strand RNA viruses characterized by club-like spikes projecting from their surface and an unusually large RNA genome3. The SARS-CoV-2 genome encodes four major structural proteins: the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein and the envelope (E) protein, each of which is essential to compose the viral particle3.  



Binding of SARS-CoV-2 to the host cell receptor

​Like all coronaviruses, SARS-CoV-2 utilizes the S glycoprotein to promote entry into the host cell. This protein contains two functional domains: an S1 receptor-binding domain (RBD), and a second S2 domain that mediates the fusion of the viral and host cell membranes4.​

SARS-CoV-2 S protein binds to the ACE2 receptor on the host cell, initially through the S1 receptor binding domain. The S1 domain is then shed from the viral surface, allowing the S2 domain to fuse to the host cell membrane. This process is dependent upon activation of the S protein, by cleavage at two sites (S1/S2 and S2’) via the proteases Furin and TMPRSS2. Furin cleavage at the S1/S2 site may lead to conformational changes in the viral S protein that exposes the RBD and/or the S2 domain. TMPRSS2 cleavage of the SARS-CoV-2 S protein is believed to enable the fusion of the viral capsid with the host cell to permit viral entry5,6. 

Exposure of the RBD in the S1 protein subunit creates an unstable subunit conformation. Consequently, during binding, this subunit undergoes conformational rearrangement between two states, known as the up and down conformations. The down state transiently hides the RBD, while the up state exposes the RBD, but temporarily destabilizes the protein subunit7,8,9. Within the trimeric S protein, only one of the three RBD is present in the accessible conformation to bind the human Angiotensin 2 (hACE2) host cell receptor10.

The critical functions of the SARS-CoV-2 S protein, ACE2, and the Furin and TMPRSS2 enzymes in binding and mediating viral entry to the host cell make these proteins key targets for drug development and viral inhibition in the efforts against COVID-19.


SARS-CoV-2 recommended products


NameAbIDApplication
Anti-SARS-CoV-2 Spike Glycoprotein S1 antibody [CR3022]ab273073Neutralising, ELISA
Recombinant Anti-SARS-CoV-2 Spike Glycoprotein S1 antibody [CR3022] - Chimericab273074Neutralising, ELISA
Human ACE2 ELISA Kitab235649ELISA
Recombinant Anti-ACE2 antibody [EPR4435(2)]ab108252IHC-P, IP, WB
Anti-ACE2 antibody [EPR4436]ab108209WB, IP, IHC-P
Recombinant Anti-TMPRSS2 antibody [EPR3862]ab109131ICC/IF, WB, IHC-P
Recombinant anti-TMPRSS2 antibody [EPR3861]ab92323WB, IHC-P
Camostat mesylate, TMPRSS2 inhibitorab145709Inhibitor
Recombinant Anti-Furin antibody [EPR14674]ab183495ICC/IF, IHC-P, WB
Naphthofluorescein, Furin inhibitorab145383Inhibitor
​


References


  1. ​Zhou P, Yang XL, Wang XG, et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). 
  2. Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). 
  3. Fehr AR and Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 1282:1-23 (2015).
  4. Walls AC, Park YJ, Tortorici MA, et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 181(2), 281-292.e6 (2020).
  5. Bestle D, Heindl MR, Limbu H et al. TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-CoV-2 in human airway epithelial cells and provide promising drug targets. bioRxiv doi: https://doi.org/10.1101/2020.04.15.042085 (2020). 
  6. Yuan M, Wu MC, Zhu X, et al. A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science 10.1126/science.abb7269 (2020).
  7. Gui M, Song W, Zhou H, et al. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res. 27, 119–129 (2017).
  8. Walls AC, Xiong X, Park YJ, et al. Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell 176, 1026–1039.e15 (2019).
  9. Walls AC, Tortorici MA, Snijder J, et al. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc. Natl. Acad. Sci. U.S.A. 114, 11157–11162 (2017).
  10. Wrapp D, Wang N, Corbett KS, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 36(6483), 1260-1263 (2020).
Zhou P, Yang XL, Wang XG, et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). 
Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). 
Fehr AR and Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 1282:1-23 (2015).
Walls AC, Park YJ, Tortorici MA, et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 181(2), 281-292.e6 (2020).
Bestle D, Heindl MR, Limbu H et al. TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-CoV-2 in human airway epithelial cells and provide promising drug targets. bioRxiv doi: https://doi.org/10.1101/2020.04.15.042085 (2020). 
Yuan M, Wu MC, Zhu X, et al. A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science 10.1126/science.abb7269 (2020).
Gui M, Song W, Zhou H, et al. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res. 27, 119–129 (2017).
Walls AC, Xiong X, Park YJ, et al. Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell 176, 1026–1039.e15 (2019).
Walls AC, Tortorici MA, Snijder J, et al. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc. Natl. Acad. Sci. U.S.A. 114, 11157–11162 (2017).
Wrapp D, Wang N, Corbett KS, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 36(6483), 1260-1263 (2020).