7JN5

Crystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Literature

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.

Wu, N.C., Yuan, M., Bangaru, S., Huang, D., Zhu, X., Lee, C.D., Turner, H.L., Peng, L., Yang, L., Burton, D.R., Nemazee, D., Ward, A.B., Wilson, I.A.

(2020) PLoS Pathog 16: e1009089-e1009089

  • DOI: 10.1371/journal.ppat.1009089
  • Primary Citation of Related Structures:  
    7JN5

  • PubMed Abstract: 

    • 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 is able to cross-react with SARS-CoV-2, but with lower affinity ...

    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 is able to 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 cross-neutralizing epitopes on SARS-like viruses.

    Organizational Affiliation: 

    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CR3022 heavy chainA [auth H]221Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CR3022 light chainB [auth L]221Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinC [auth F]230Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59594
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F 2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
E [auth H]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.736α = 90
b = 59.931β = 99.77
c = 51.721γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI139445
Bill & Melinda Gates FoundationOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI44462

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references