7SN1

Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.

Nabel, K.G.Clark, S.A.Shankar, S.Pan, J.Clark, L.E.Yang, P.Coscia, A.McKay, L.G.A.Varnum, H.H.Brusic, V.Tolan, N.V.Zhou, G.Desjardins, M.Turbett, S.E.Kanjilal, S.Sherman, A.C.Dighe, A.LaRocque, R.C.Ryan, E.T.Tylek, C.Cohen-Solal, J.F.Darcy, A.T.Tavella, D.Clabbers, A.Fan, Y.Griffiths, A.Correia, I.R.Seagal, J.Baden, L.R.Charles, R.C.Abraham, J.

(2022) Science 375: eabl6251-eabl6251

  • DOI: https://doi.org/10.1126/science.abl6251
  • Primary Citation of Related Structures:  
    7SN0, 7SN1, 7SN2, 7SN3

  • PubMed Abstract: 

    Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.


  • Organizational Affiliation

    Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
neutralizing antibody C1C-A3 Fab heavy chainA [auth H]250Homo sapiensMutation(s): 0 
Gene Names: IGHV3-33
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
neutralizing antibody C1C-A3 Fab light chainB [auth L]238Homo sapiensMutation(s): 0 
Gene Names: IGKV3-11
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: 1.47 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.736α = 90
b = 52.369β = 113.69
c = 71.394γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Omodel building
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Statesno grant number

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2022-02-02
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary