7U0E

Crystal Structure of C13C9 Fab in complex with SARS-CoV-2 S fusion peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 C13C9A,
E [auth H]		229Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain Fab C13C9B,
F [auth L]		213Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SARS-CoV-2 S fusion peptideC, D13Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.898α = 96.5
b = 65.682β = 108.06
c = 71.001γ = 110.52
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 2.0: 2022-08-10
    Changes: Advisory, Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary