Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds the receptor angiotensin converting enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its S2 domain. Whereas the S1 domain contains high sequence variability, the S2 domain is conserved and is a promising pan-betacoronavirus vaccine target. We applied cryo-electron tomography to capture intermediates of S2 refolding and understand inhibition by antibodies to the S2 stem-helix. Subtomogram averaging revealed ACE2 dimers cross-linking spikes before transitioning into S2 intermediates, which were captured at various stages of refolding. Pan-betacoronavirus neutralizing antibodies targeting the S2 stem-helix bound to and inhibited refolding of spike prehairpin intermediates. Combined with molecular dynamics simulations, these structures elucidate the process of SARS-CoV-2 entry and reveal how pan-betacoronavirus S2-targeting antibodies neutralize infectivity by arresting prehairpin intermediates.
MeSH terms
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Angiotensin-Converting Enzyme 2* / chemistry
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Angiotensin-Converting Enzyme 2* / metabolism
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Antibodies, Neutralizing* / chemistry
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Antibodies, Neutralizing* / immunology
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Antibodies, Viral* / chemistry
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Antibodies, Viral* / immunology
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Betacoronavirus / chemistry
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Betacoronavirus / immunology
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COVID-19 / immunology
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COVID-19 / virology
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Cell Membrane / metabolism
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Cryoelectron Microscopy*
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Electron Microscope Tomography
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Humans
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Molecular Dynamics Simulation*
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Peptidyl-Dipeptidase A / chemistry
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Peptidyl-Dipeptidase A / metabolism
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Protein Domains*
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Protein Multimerization
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Protein Refolding
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SARS-CoV-2* / genetics
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SARS-CoV-2* / immunology
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Spike Glycoprotein, Coronavirus* / chemistry
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Spike Glycoprotein, Coronavirus* / genetics
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Spike Glycoprotein, Coronavirus* / immunology
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Spike Glycoprotein, Coronavirus* / metabolism
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Virus Internalization
Substances
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Spike Glycoprotein, Coronavirus
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spike protein, SARS-CoV-2
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Angiotensin-Converting Enzyme 2
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Antibodies, Neutralizing
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ACE2 protein, human
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Antibodies, Viral
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Peptidyl-Dipeptidase A