8QH0 | pdb_00008qh0

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.209 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2.

Planchais, C.Fernandez, I.Chalopin, B.Bruel, T.Rosenbaum, P.Beretta, M.Dimitrov, J.D.Conquet, L.Donati, F.Prot, M.Porrot, F.Planas, D.Staropoli, I.Guivel-Benhassine, F.Baquero, E.van der Werf, S.Haouz, A.Simon-Loriere, E.Montagutelli, X.Maillere, B.Rey, F.A.Guardado-Calvo, P.Nozach, H.Schwartz, O.Mouquet, H.

(2024) iScience 27: 110354-110354

  • DOI: https://doi.org/10.1016/j.isci.2024.110354
  • Primary Citation of Related Structures:  
    8QH0, 8QH1

  • PubMed Abstract: 

    Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1206Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: S2
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cv2.3194 Heavy chainB [auth H]229Homo sapiensMutation(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
IGK@ proteinC [auth L]211Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PJF2 (Homo sapiens)
Explore Q6PJF2 
Go to UniProtKB:  Q6PJF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJF2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.209 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.388α = 90
b = 89.186β = 90
c = 174.471γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary
  • Version 1.2: 2025-07-02
    Changes: Database references