7U09

Crystal Structure of C13B8 Fab in complex with SARS-CoV-2 S fusion peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.

Low, J.S.Jerak, J.Tortorici, M.A.McCallum, M.Pinto, D.Cassotta, A.Foglierini, M.Mele, F.Abdelnabi, R.Weynand, B.Noack, J.Montiel-Ruiz, M.Bianchi, S.Benigni, F.Sprugasci, N.Joshi, A.Bowen, J.E.Stewart, C.Rexhepaj, M.Walls, A.C.Jarrossay, D.Morone, D.Paparoditis, P.Garzoni, C.Ferrari, P.Ceschi, A.Neyts, J.Purcell, L.A.Snell, G.Corti, D.Lanzavecchia, A.Veesler, D.Sallusto, F.

(2022) Science : eabq2679-eabq2679

  • DOI: 10.1126/science.abq2679
  • Primary Citation of Related Structures:  
    7SKZ, 7SL5, 7U09, 7U0A, 7U0E

  • PubMed Abstract: 
  • The coronavirus spike (S) glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus S proteins ...

    The coronavirus spike (S) glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus S proteins. This class of mAbs recognize the fusion peptide and acquire affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha- and beta-coronaviruses, including animal coronavirus WIV-1 and PDF-2180. Two selected mAbs also neutralize Omicron BA.1 and BA.2 authentic viruses and reduce viral burden and pathology in vivo. Structural and functional analyses show that the fusion peptide-specific mAbs bind with different modalities to a cryptic epitope, which is hidden in prefusion stabilized S, and becomes exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.


    Organizational Affiliation

    Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain Fab C13B8A [auth H]229Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain Fab C13B8B [auth L]213Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SARS-CoV-2 S fusion peptideC [auth A]14Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.269α = 90
b = 69.323β = 90
c = 150.694γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Partnership for Structural Biology (PSB)FranceSSGCID

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Source and taxonomy