Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Open accessAbstract
SUMMARY: The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike (S) glycoprotein trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2, establishing ACE2 as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S 1 /S 2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.
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The SARS-CoV-2 Spike protein mediates binding of coronaviruses to ACE2 on the surface of various cell types including epithelial cells of the pulmonary alveolus.
“The S protein mediates binding of coronaviruses to angiotensin converting enzyme 2 (ACE2) on the surface of various cell types including epithelial cells of the pulmonary alveolus (4–6).”
From An <i>Alphavirus</i> -derived replicon RNA vaccine induces SARS-CoV-2 neutralizing antibody and T cell responses in mice and nonhuman primates (2020) · cites this paper as [6]
The Introduction and Results section “ACE2 Is an Entry Receptor for SARS-CoV-2” establish that SARS-CoV-2 spike binds ACE2 and can mediate entry into ACE2-expressing cells. The same Results section identifies ACE2 at the surface of type II pneumocytes—alveolar epithelial cells—but makes that statement about SARS-CoV, not SARS-CoV-2. The cited paper therefore does not directly establish SARS-CoV-2 spike binding on those lung cells. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMost neutralizing antibodies are molded based on epitopes of S protein in prefusion conformation, which is covered once the S protein acquires the postfusion conformation, thus reducing the production of neutralizing antibodies.
“Most neutralizing antibodies are molded based on epitopes of S protein in prefusion conformation, which is covered once the S protein acquires the postfusion conformation, thus reducing the production of neutralizing antibodies.238”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [238]
The S1/S2 cleavage site strategy employs direct deletion of the sequence Q677TNSPRRARYSV687 to Q677TILRYSV683 or mutation of amino acids (RRAR to GGSG) that prevent S protein cleavage in the host cell, thus maintaining its structural stability and inducing stronger immune responses.
“The S1/S2 cleavage site strategy employs direct deletion of the sequence Q677TNSPRRARYSV687 in wild-type SARS-CoV-2 protein S to Q677TILRYSV683238 or mutation of amino acids (RRAR to GGSG)141 that ultimately prevent the S protein from cleavage in the host cell, thus maintaining its structural stability and inducing stronger immune responses.”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [238]
BNT162b1 encodes a trimerized, secreted version of the spike protein's receptor-binding domain.
“BNT162b1 encodes a trimerized, secreted version of the spike protein’s receptor-binding domain, whereas BNT162b2 encodes the full-length SARS-CoV-2 spike glycoprotein with two proline substitutions in the S2 subunit, which lock the protein in its prefusion conformation120,121.”
From mRNA vaccines for infectious diseases: principles, delivery and clinical translation (2021) · cites this paper as [121]
BNT162b2 encodes the full-length SARS-CoV-2 spike glycoprotein with two proline substitutions in the S2 subunit, which lock the protein in its prefusion conformation.
“BNT162b1 encodes a trimerized, secreted version of the spike protein’s receptor-binding domain, whereas BNT162b2 encodes the full-length SARS-CoV-2 spike glycoprotein with two proline substitutions in the S2 subunit, which lock the protein in its prefusion conformation120,121.”
From mRNA vaccines for infectious diseases: principles, delivery and clinical translation (2021) · cites this paper as [121]
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The human coronavirus HCoV-229E S-protein structure and receptor binding
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Receptor-binding loops in alphacoronavirus adaptation and evolution
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Automatically Fixing Errors in Glycoprotein Structures with Rosetta
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Murine Leukemia Virus (MLV)-based Coronavirus Spike-pseudotyped Particle Production and Infection
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Self-citationThe Structure of HPK1 Kinase Domain: To Boldly Go Where No Immuno-Oncology Drugs Have Gone Before
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Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
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The proximal origin of SARS-CoV-2
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The trinity of COVID-19: immunity, inflammation and intervention
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Structural basis of receptor recognition by SARS-CoV-2
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Extrapulmonary manifestations of COVID-19
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Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2
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“Notably, two cryo-EM structures of trimeric SARS-CoV-2 S proteins were also published recently, with the receptor binding region buried or exposed (Walls et al., 2020; Wrapp et al., 2020), which is consistent with the structural features of MERS-CoV and SARS-CoV S proteins (Yuan et al.”
Cell entry mechanisms of SARS-CoV-2
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Self-citationHuman organoids: model systems for human biology and medicine
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Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity
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A serological assay to detect SARS-CoV-2 seroconversion in humans
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Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody
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Convergent Antibody Responses to SARS-CoV-2 in Convalescent Individuals
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Human neutralizing antibodies elicited by SARS-CoV-2 infection
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The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity
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Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike
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SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
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A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2
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SARS-CoV-2 productively infects human gut enterocytes
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mRNA vaccines for infectious diseases: principles, delivery and clinical translation
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Immunology of COVID-19: Current State of the Science
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Structure-based design of prefusion-stabilized SARS-CoV-2 spikes
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Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail
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SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract
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SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19
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Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability
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Neuropilin-1 is a host factor for SARS-CoV-2 infection
Daly, J. L., Simonetti, B., Klein, K., Chen, K.-E., Williamson, M. K., Antón-Plágaro, C., Shoemark, D. K., Simón-Gracia, L., Bauer, M., Hollandi, R., et al. (2020) · Science · doi:10.1126/science.abd3072 · Cited by 1,251 · see citing works
The pivotal link between ACE2 deficiency and SARS-CoV-2 infection
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“The present review discusses the role of angiotensin converting enzyme 2 (ACE2) receptors which are not only the door through which the virus enters into cells, [2,3] but also the conductor of several pathophysiological reactions associated with the clinical features of the disease, with potential therapeutic implicat…”
InfluentialDistinct conformational states of SARS-CoV-2 spike protein
Cai, Y., Zhang, J., Xiao, T., Peng, H., Sterling, S. M., Walsh, R. M., Rawson, S., Rits-Volloch, S., & Chen, B. (2020) · Science · doi:10.1126/science.abd4251 · Cited by 1,221 · see citing works
Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Yin, W., Mao, C., Luan, X., Shen, D.-D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., et al. (2020) · Science · doi:10.1126/science.abc1560 · Cited by 1,219 · see citing works
Potently neutralizing and protective human antibodies against SARS-CoV-2
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Why does COVID-19 disproportionately affect older people?
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SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147 · see citing works
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Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
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SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity
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Molecular Architecture of the SARS-CoV-2 Virus
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“Native Structures of S in the Prefusion Conformation The native structures of S in the ‘‘RBD down’’ and ‘‘one RBD up’’ conformations were similar to the rigidly fitted recombinant protein structures (PDB: 6XR8, 6VYB; Cai et al., 2020; Walls et al., 2020), except for the N terminus domain (NTD).”
InfluentialN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901 · see citing works
“The in vitro neutralization activity of the NTD-specific mAbs was subsequently evaluated using a SARS-CoV-2 S pseudotyped murine leukemia virus (MLV) system (Millet and Whittaker, 2016; Walls et al., 2020b).”
InfluentialSelf-citationThe biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009 · see citing works
TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes
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SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
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- Authors
- Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D.
- Affiliations
- University of Washington (US)
- Fred Hutch Cancer Center (US)
- Corresponding author
- Veesler, David
- Venue
- Cell
- Publisher
- openRxiv
- Published
- 2020-02-20
- Volume
- 181
- Issue
- 2
- Pages
- 281-292.e6
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7102599
- OpenAlex
- W3009335299
- Cited by
- 8,586
- References
- 105
- Citations by year
- 2026: 220 · 2025: 378 · 2024: 621 · 2023: 877 · 2022: 1524 · 2021: 2686 · 2020: 2265 · 2019: 3 · 2013: 1 · 2012: 2
- FWCI
- 241.19
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Burroughs Wellcome Fund
- National Institutes of Health (1s10od023476-01)
- National Institute of General Medical Sciences (R01GM120553)
- National Institute of Allergy and Infectious Diseases (HHSN272201700059C)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, spike protein, ACE2 receptor, receptor binding domain, furin cleavage site, viral entry, cross-neutralizing antibodies, SARS-CoV, vaccine design, antiviral agents, cryo-EM structure, antigenicity
- MeSH terms
- Betacoronavirus, Angiotensin-Converting Enzyme 2, SARS-CoV-2, Amino Acid Sequence, Antigens, Viral, Cell Line, Humans, Peptidyl-Dipeptidase A, Models, Molecular, Receptors, Virus, Cryoelectron Microscopy, Severe acute respiratory syndrome-related coronavirus, Virus Internalization, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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