7TE1

SARS-CoV-2 Receptor Binding Domain in Complex with Ab17

  • Classification: IMMUNE SYSTEM/Viral Protein
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-01-03 Released: 2022-03-30 
  • Deposition Author(s): Hauser, B.M., Schmidt, A.G.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.299 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting.

Hauser, B.M.Sangesland, M.St Denis, K.J.Lam, E.C.Case, J.B.Windsor, I.W.Feldman, J.Caradonna, T.M.Kannegieter, T.Diamond, M.S.Balazs, A.B.Lingwood, D.Schmidt, A.G.

(2022) Cell Rep 38: 110561-110561

  • DOI: https://doi.org/10.1016/j.celrep.2022.110561
  • Primary Citation of Related Structures:  
    7TE1

  • PubMed Abstract: 

    Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit the spread of related viruses with pandemic potential. Here we leverage rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding in boosting immunogens, we focus murine serum antibody responses to conserved receptor binding motif (RBM) and receptor binding domain (RBD) epitopes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike imprinting. Although all engineered immunogens elicit a robust SARS-CoV-2-neutralizing serum response, RBM-focusing immunogens exhibit increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defines a conserved epitope. RBM-focused sera confer protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. These engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes.


  • Organizational Affiliation

    Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ab17 heavy chainA [auth C],
C [auth H]
223Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ab17 light chainB [auth F],
D [auth L]
214Homo 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
Spike protein S1E [auth D],
F [auth E]
211Homo sapiensMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.299 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.931α = 90
b = 207.931β = 90
c = 86.662γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling

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 StatesR01 AI146779
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF30 AI160908
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM007753

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary