7SL5

Crystal Structure of VP12E7 Fab in complex with SARS-CoV-2 S fusion peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 2.3 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 377: 735-742

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

  • PubMed Abstract: 

    The coronavirus spike glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus spike proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors. These 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 betacoronaviruses, including animal coronaviruses 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 showed that the fusion peptide-specific mAbs bound with different modalities to a cryptic epitope hidden in prefusion stabilized spike, which became exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.


  • Organizational Affiliation

    Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain VP12E7 Fab
A, D, G, J
235Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain VP12E7 Fab
B, E, H, K
215Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN
C, F, I, L
15Severe 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  
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UniProt GroupP0DTC2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.148α = 90.34
b = 81.359β = 95.96
c = 95.65γ = 100.65
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Source and taxonomy
  • Version 2.0: 2022-08-03
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2022-08-10
    Changes: Database references
  • Version 2.2: 2022-08-24
    Changes: Database references
  • Version 2.3: 2023-10-18
    Changes: Data collection, Refinement description