8D36

Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody COV44-62


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutralizing antibody COV44-62 heavy chainA [auth H]227Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neutralizing antibody COV44-62 light chainB [auth L]216Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S2 fusion peptideC [auth F]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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.535α = 90
b = 71.915β = 114.16
c = 76.258γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
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
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary