7TTX

Crystal structure of potent neutralizing antibody 10-40 in complex with Sarbecovirus bat RaTG13 receptor-binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses.

Liu, L.Iketani, S.Guo, Y.Reddem, E.R.Casner, R.G.Nair, M.S.Yu, J.Chan, J.F.Wang, M.Cerutti, G.Li, Z.Morano, N.C.Castagna, C.D.Corredor, L.Chu, H.Yuan, S.Poon, V.K.Chan, C.C.Chen, Z.Luo, Y.Cunningham, M.Chavez, A.Yin, M.T.Perlin, D.S.Tsuji, M.Yuen, K.Y.Kwong, P.D.Sheng, Z.Huang, Y.Shapiro, L.Ho, D.D.

(2022) Sci Transl Med 14: eabn6859-eabn6859

  • DOI: https://doi.org/10.1126/scitranslmed.abn6859
  • Primary Citation of Related Structures:  
    7SD5, 7SI2, 7TTM, 7TTX, 7TTY

  • PubMed Abstract: 

    The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.


  • Organizational Affiliation

    Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein231Bat coronavirus RaTG13Mutation(s): 0 
UniProt
Find proteins for A0A6B9WHD3 (Bat coronavirus RaTG13)
Explore A0A6B9WHD3 
Go to UniProtKB:  A0A6B9WHD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6B9WHD3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1040 heavy chainB [auth H]237Homo 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
1040 light chainC [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.174α = 90
b = 76.816β = 90
c = 117.626γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Jack Ma FoundationChina--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2022-06-08
    Changes: Database references
  • Version 1.3: 2022-08-10
    Changes: Structure summary
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description