7XSW

Structure of SARS-CoV-2 antibody S309 with GX/P2V/2017 RBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.281 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017.

Jia, Y.Niu, S.Hu, Y.Chai, Y.Zheng, A.Su, C.Wu, L.Han, P.Han, P.Lu, D.Liu, Z.Yan, X.Tian, D.Chen, Z.Qi, J.Tian, W.X.Wang, Q.Gao, G.F.

(2022) Cell Rep 41: 111831-111831

  • DOI: https://doi.org/10.1016/j.celrep.2022.111831
  • Primary Citation of Related Structures:  
    7XNF, 7XSW

  • PubMed Abstract: 

    Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, multiple SARS-CoV-2-related viruses have been characterized, including pangolin-origin GD/1/2019 and GX/P2V/2017. Our previous study indicated that both viruses have the potential to infect humans. Here, we find that CB6 (commercial name etesevimab), a COVID-19 therapeutic monoclonal antibody (MAb) developed by our group, efficiently inhibits GD/1/2019 but not GX/P2V/2017. A total of 50 SARS-CoV-2 MAbs divided into seven groups based on their receptor-binding domain (RBD) epitopes, together with the COVID-19 convalescent sera, are systematically screened for their cross-binding and cross-neutralizing properties against GX/P2V/2017. We find that GX/P2V/2017 displays substantial immune difference from SARS-CoV-2. Furthermore, we solve two complex structures of the GX/P2V/2017 RBD with MAbs belonging to RBD-1 and RBD-5, providing a structural basis for their different antigenicity. These results highlight the necessity for broad anti-coronavirus countermeasures and shed light on potential therapeutic targets.


  • Organizational Affiliation

    College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S309 Heavy ChainA [auth H],
D [auth A]
237Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S309 Lambda ChainB [auth L],
E [auth B]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1C [auth R],
F [auth C]
215Pangolin coronavirusMutation(s): 0 
UniProt
Find proteins for A0A6G9KP06 (Pangolin coronavirus)
Explore A0A6G9KP06 
Go to UniProtKB:  A0A6G9KP06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6G9KP06
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.281 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.639α = 110.527
b = 73.599β = 92.075
c = 105.615γ = 97.049
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary