4XVJ

STRUCTURE OF THE HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN E2 ANTIGENIC 2 REGION 412-423 BOUND TO THE BROADLY NEUTRALIZING ANTIBODY HC33.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for penetration of the glycan shield of hepatitis C virus e2 glycoprotein by a broadly neutralizing human antibody.

Li, Y.Pierce, B.G.Wang, Q.Keck, Z.Y.Fuerst, T.R.Foung, S.K.Mariuzza, R.A.

(2015) J Biol Chem 290: 10117-10125

  • DOI: https://doi.org/10.1074/jbc.M115.643528
  • Primary Citation of Related Structures:  
    4XVJ

  • PubMed Abstract: 

    Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. A challenge for HCV vaccine development is to identify conserved epitopes able to elicit protective antibodies against this highly diverse virus. Glycan shielding is a mechanism by which HCV masks such epitopes on its E2 envelope glycoprotein. Antibodies to the E2 region comprising residues 412-423 (E2(412-423)) have broadly neutralizing activities. However, an adaptive mutation in this linear epitope, N417S, is associated with a glycosylation shift from Asn-417 to Asn-415 that enables HCV to escape neutralization by mAbs such as HCV1 and AP33. By contrast, the human mAb HC33.1 can neutralize virus bearing the N417S mutation. To understand how HC33.1 penetrates the glycan shield created by the glycosylation shift to Asn-415, we determined the structure of this broadly neutralizing mAb in complex with its E2(412-423) epitope to 2.0 Å resolution. The conformation of E2(412-423) bound to HC33.1 is distinct from the β-hairpin conformation of this peptide bound to HCV1 or AP33, because of disruption of the β-hairpin through interactions with the unusually long complementarity-determining region 3 of the HC33.1 heavy chain. Whereas Asn-415 is buried by HCV1 and AP33, it is solvent-exposed in the HC33.1-E2(412-423) complex, such that glycosylation of Asn-415 would not prevent antibody binding. Furthermore, our results highlight the structural flexibility of the E2(412-423) epitope, which may serve as an immune evasion strategy to impede induction of antibodies targeting this site by reducing its antigenicity.


  • Organizational Affiliation

    From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HCV E2 antigen13Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27958
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody heavy chain variable domainB [auth H]141Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
antibody light chain variable domainC [auth L]115Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.085α = 90
b = 53.728β = 90
c = 107.238γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Database references
  • Version 1.3: 2016-07-27
    Changes: Data collection
  • Version 1.4: 2016-12-28
    Changes: Structure summary
  • Version 1.5: 2024-10-23
    Changes: Data collection, Database references, Structure summary