4HS8

Hepatitus C envelope glycoprotein E2 fragment 412-423 with humanized and affinity-matured antibody hu5B3.v3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 

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
  • Primary Citation of Related Structures:  4HS6

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E2-peptide
A
16Hepatitis C virusN/A
Find proteins for Q9YK84 (Hepatitis C virus)
Go to UniProtKB:  Q9YK84
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody hu5B3.v2 Fab heavy chain
H
228N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody hu5B3.v2 Fab light chain
L
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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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: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.716α = 90.00
b = 77.716β = 90.00
c = 181.384γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling
HKL-2000data reduction
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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