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TitleA natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.
Journal, issue, pagesbioRxiv, Year 2020
Publish dateSep 21, 2020
AuthorsNicholas C Wu / Meng Yuan / Sandhya Bangaru / Deli Huang / Xueyong Zhu / Chang-Chun D Lee / Hannah L Turner / Linghang Peng / Linlin Yang / David Nemazee / Andrew B Ward / Ian A Wilson /
PubMed AbstractEpitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly ...Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that can cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential for cross-neutralizing epitopes on SARS-like viruses.
External linksbioRxiv / PubMed:32995788 / PubMed Central
MethodsEM (single particle)
Resolution6.15 - 24.0 Å
Structure data

EMDB-22858:
SARS-CoV spike in complex with CR3022 Fab (1 Fab bound)
Method: EM (single particle) / Resolution: 24.0 Å

EMDB-22859:
SARS-CoV spike in complex with CR3022 Fab (2 Fab bound)
Method: EM (single particle) / Resolution: 22.9 Å

EMDB-22860:
SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)
Method: EM (single particle) / Resolution: 24.0 Å

EMDB-22861:
Structure of SARS-CoV spike in complex with CR3022 Fab (Class 1)
Method: EM (single particle) / Resolution: 6.83 Å

EMDB-22862:
Structure of SARS-CoV spike in complex with CR3022 Fab (Class 2)
Method: EM (single particle) / Resolution: 6.24 Å

EMDB-22863:
Structure of SARS-CoV spike in complex with CR3022 Fab (Class 3)
Method: EM (single particle) / Resolution: 6.42 Å

EMDB-22864:
Structure of SARS-CoV spike in complex with CR3022 Fab (Class 4)
Method: EM (single particle) / Resolution: 6.15 Å

Source
  • Severe acute respiratory syndrome-related coronavirus

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