4HS6

Hepatitus C envelope glycoprotein E2 fragment 412-423 with humanized and affinity-matured antibody MRCT10.v362


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Glycan shifting on hepatitis C virus (HCV) e2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies.

Pantua, H.Diao, J.Ultsch, M.Hazen, M.Mathieu, M.McCutcheon, K.Takeda, K.Date, S.Cheung, T.K.Phung, Q.Hass, P.Arnott, D.Hongo, J.A.Matthews, D.J.Brown, A.Patel, A.H.Kelley, R.F.Eigenbrot, C.Kapadia, S.B.

(2013) J Mol Biol 425: 1899-1914

  • DOI: 10.1016/j.jmb.2013.02.025
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Hepatitis C virus (HCV) infection is a major cause of liver disease and hepatocellular carcinoma. Glycan shielding has been proposed to be a mechanism by which HCV masks broadly neutralizing epitopes on its viral glycoproteins. However, the role of a ...

    Hepatitis C virus (HCV) infection is a major cause of liver disease and hepatocellular carcinoma. Glycan shielding has been proposed to be a mechanism by which HCV masks broadly neutralizing epitopes on its viral glycoproteins. However, the role of altered glycosylation in HCV resistance to broadly neutralizing antibodies is not fully understood. Here, we have generated potent HCV neutralizing antibodies hu5B3.v3 and MRCT10.v362 that, similar to the previously described AP33 and HCV1, bind to a highly conserved linear epitope on E2. We utilize a combination of in vitro resistance selections using the cell culture infectious HCV and structural analyses to identify mechanisms of HCV resistance to hu5B3.v3 and MRCT10.v362. Ultra deep sequencing from in vitro HCV resistance selection studies identified resistance mutations at asparagine N417 (N417S, N417T and N417G) as early as 5days post treatment. Comparison of the glycosylation status of soluble versions of the E2 glycoprotein containing the respective resistance mutations revealed a glycosylation shift from N417 to N415 in the N417S and N417T E2 proteins. The N417G E2 variant was glycosylated neither at residue 415 nor at residue 417 and remained sensitive to MRCT10.v362. Structural analyses of the E2 epitope bound to hu5B3.v3 Fab and MRCT10.v362 Fab using X-ray crystallography confirmed that residue N415 is buried within the antibody-peptide interface. Thus, in addition to previously described mutations at N415 that abrogate the β-hairpin structure of this E2 linear epitope, we identify a second escape mechanism, termed glycan shifting, that decreases the efficacy of broadly neutralizing HCV antibodies.


    Organizational Affiliation

    Department of Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: kapadia.sharookh@gene.com.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E2-peptideY, Z16Hepacivirus CMutation(s): 0 
Find proteins for Q9YK84 (Hepacivirus C)
Explore Q9YK84 
Go to UniProtKB:  Q9YK84
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MRCT10.v362 Fab light chainA, L218Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MRCT10.v362 Fab heavy chainB, H226Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.091α = 90
b = 90.821β = 109.35
c = 72.681γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references