8DAO

Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Broadly neutralizing antibodies target the coronavirus fusion peptide.

Dacon, C.Tucker, C.Peng, L.Lee, C.D.Lin, T.H.Yuan, M.Cong, Y.Wang, L.Purser, L.Williams, J.K.Pyo, C.W.Kosik, I.Hu, Z.Zhao, M.Mohan, D.Cooper, A.J.R.Peterson, M.Skinner, J.Dixit, S.Kollins, E.Huzella, L.Perry, D.Byrum, R.Lembirik, S.Drawbaugh, D.Eaton, B.Zhang, Y.Yang, E.S.Chen, M.Leung, K.Weinberg, R.S.Pegu, A.Geraghty, D.E.Davidson, E.Douagi, I.Moir, S.Yewdell, J.W.Schmaljohn, C.Crompton, P.D.Holbrook, M.R.Nemazee, D.Mascola, J.R.Wilson, I.A.Tan, J.

(2022) Science 377: 728-735

  • DOI: https://doi.org/10.1126/science.abq3773
  • Primary Citation of Related Structures:  
    8D36, 8D6Z, 8DAO

  • PubMed Abstract: 

    The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain-specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2' cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.


  • Organizational Affiliation

    Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COV44-79 heavy chain variable domainA [auth C],
F [auth A]
126Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COV44-79 light chain variable domainB [auth D],
G [auth B]
109Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COV44-79 heavy chain constant domainC [auth E],
H [auth G]
103Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COV44-79 light chain constant domainD [auth F],
I [auth H]
107Homo sapiensMutation(s): 0 
Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
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PHAROS:  P01834
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S2 fusion peptideE [auth I],
J
15Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.368α = 90
b = 100.368β = 90
c = 229.939γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary