7M53

B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for broad coronavirus neutralization.

Sauer, M.M.Tortorici, M.A.Park, Y.J.Walls, A.C.Homad, L.Acton, O.J.Bowen, J.E.Wang, C.Xiong, X.de van der Schueren, W.Quispe, J.Hoffstrom, B.G.Bosch, B.J.McGuire, A.T.Veesler, D.

(2021) Nat Struct Mol Biol 28: 478-486

  • DOI: https://doi.org/10.1038/s41594-021-00596-4
  • Primary Citation of Related Structures:  
    7M51, 7M52, 7M53, 7M55, 7M5E

  • PubMed Abstract: 

    Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein stem helix peptide16Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
B6 antigen-binding (Fab) fragment heavy chainB [auth H]220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
B6 antigen-binding (Fab) fragment light chainC [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.183α = 90
b = 60.36β = 93.63
c = 79.699γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Structure summary
  • Version 1.2: 2021-06-23
    Changes: Database references, Structure summary
  • Version 1.3: 2021-06-30
    Changes: Structure summary
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary