5VXR

The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Escape of Hepatitis C Virus from Epitope I Neutralization Increases Sensitivity of Other Neutralization Epitopes.

Gu, J.Hardy, J.Boo, I.Vietheer, P.McCaffrey, K.Alhammad, Y.Chopra, A.Gaudieri, S.Poumbourios, P.Coulibaly, F.Drummer, H.E.

(2018) J. Virol. 92: --

  • DOI: 10.1128/JVI.02066-17

  • PubMed Abstract: 
  • The hepatitis C virus (HCV) E2 glycoprotein is a major target of the neutralizing antibody (nAb) response, with multiple type-specific and broadly neutralizing antibody (bnAb) epitopes identified. The 412-to-423 region can generate bnAbs that block i ...

    The hepatitis C virus (HCV) E2 glycoprotein is a major target of the neutralizing antibody (nAb) response, with multiple type-specific and broadly neutralizing antibody (bnAb) epitopes identified. The 412-to-423 region can generate bnAbs that block interaction with the cell surface receptor CD81, with activity toward multiple HCV genotypes. In this study, we reveal the structure of rodent monoclonal antibody 24 (MAb24) with an extensive contact area toward a peptide spanning the 412-to-423 region. The crystal structure of the MAb24-peptide 412-to-423 complex reveals the paratope bound to a peptide hairpin highly similar to that observed with human MAb HCV1 and rodent MAb AP33, but with a different angle of approach. In viral outgrowth experiments, we demonstrated three distinct genotype 2a viral populations that acquired resistance to MAb24 via N415D, N417S, and N415D/H386R mutations. Importantly, the MAb24-resistant viruses exhibited significant increases in sensitivity to the majority of bnAbs directed to epitopes within the 412-to-423 region and in additional antigenic determinants located within E2 and the E1E2 complex. This study suggests that modification of N415 causes a global change in glycoprotein structure that increases its vulnerability to neutralization by other antibodies. This finding suggests that in the context of an antibody response to viral infection, acquisition of escape mutations in the 412-to-423 region renders the virus more susceptible to neutralization by other specificities of nAbs, effectively reducing the immunological fitness of the virus. A vaccine for HCV that generates polyspecific humoral immunity with specificity for the 412-to-423 region and at least one other region of E2 is desirable. IMPORTANCE Understanding how antibodies neutralize hepatitis C virus (HCV) is essential for vaccine development. This study reveals for the first time that when HCV develops resistance to a major class of bnAbs targeting the 412-to-423 region of E2, this results in a concomitant increase in sensitivity to neutralization by a majority of other bnAb specificities. Vaccines for the prevention of HCV infection should therefore generate bnAbs directed toward the 412-to-423 region of E2 and additional bnAb epitopes within the viral glycoproteins.


    Organizational Affiliation

    Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia.,Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia fasseli.coulibaly@monash.edu heidi.drummer@burnet.edu.au.,Virus Entry and Vaccines Laboratory, Life Sciences, Burnet Institute, Melbourne, Australia fasseli.coulibaly@monash.edu heidi.drummer@burnet.edu.au.,Virus Entry and Vaccines Laboratory, Life Sciences, Burnet Institute, Melbourne, Australia.,Department of Microbiology and Immunology at the Peter Doherty Institute, The University of Melbourne, Melbourne, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia.,Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,School of Human Sciences, University of Western Australia, Nedlands, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain
H
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAb24 Variable Light Chain,MAb24 Variable Light Chain
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Virus Envelope Protein 2
P
12Hepatitis C virus (isolate Glasgow)Mutation(s): 0 
Find proteins for Q5EG65 (Hepatitis C virus (isolate Glasgow))
Go to UniProtKB:  Q5EG65
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.370α = 90.00
b = 53.338β = 93.53
c = 133.903γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaFT1210893

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references