7RNJ

S2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Broad betacoronavirus neutralization by a stem helix-specific human antibody.

Pinto, D.Sauer, M.M.Czudnochowski, N.Low, J.S.Tortorici, M.A.Housley, M.P.Noack, J.Walls, A.C.Bowen, J.E.Guarino, B.Rosen, L.E.di Iulio, J.Jerak, J.Kaiser, H.Islam, S.Jaconi, S.Sprugasci, N.Culap, K.Abdelnabi, R.Foo, C.Coelmont, L.Bartha, I.Bianchi, S.Silacci-Fregni, C.Bassi, J.Marzi, R.Vetti, E.Cassotta, A.Ceschi, A.Ferrari, P.Cippa, P.E.Giannini, O.Ceruti, S.Garzoni, C.Riva, A.Benigni, F.Cameroni, E.Piccoli, L.Pizzuto, M.S.Smithey, M.Hong, D.Telenti, A.Lempp, F.A.Neyts, J.Havenar-Daughton, C.Lanzavecchia, A.Sallusto, F.Snell, G.Virgin, H.W.Beltramello, M.Corti, D.Veesler, D.

(2021) Science 373: 1109-1116

  • DOI: https://doi.org/10.1126/science.abj3321
  • Primary Citation of Related Structures:  
    7RNJ

  • PubMed Abstract: 

    The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.


  • Organizational Affiliation

    Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody S2P6 Fab light chainA [auth L]217Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody S2P6 Fab heavy chainB [auth H]221Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein stem helix peptideC [auth B]14Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.642α = 90
b = 92.642β = 90
c = 223.408γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description