8TFE | pdb_00008tfe

Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers.

Shahid, S.Karade, S.S.Hasan, S.S.Yin, R.Jiang, L.Liu, Y.Felbinger, N.Kulakova, L.Toth, E.A.Keck, Z.Y.Foung, S.K.H.Fuerst, T.R.Pierce, B.G.Mariuzza, R.A.

(2025) Commun Biol 8: 825-825

  • DOI: https://doi.org/10.1038/s42003-025-08239-w
  • Primary Citation of Related Structures:  
    8TFE, 8TGV, 8TGZ, 8THZ, 8TXQ, 8TZY, 8U9Y

  • PubMed Abstract: 

    Global elimination of hepatitis C virus (HCV) will require an effective cross-genotype vaccine. The HCV E2 envelope glycoprotein is the main target of neutralizing antibodies but also contains epitopes that elicit non-neutralizing antibodies which may provide protection through Fc effector functions rather than direct neutralization. We determined cryo-EM structures of a broadly neutralizing antibody, a moderately neutralizing antibody, and a non-neutralizing antibody bound to E2 to resolutions of 3.8, 3.3, and 3.7 Å, respectively. Whereas the broadly neutralizing antibody targeted the front layer of E2 and the non-neutralizing antibody targeted the back layer, the moderately neutralizing antibody straddled both front and back layers, and thereby defined a new neutralizing epitope on E2. The small size of complexes between conventional (monovalent) Fabs and E2 (~110 kDa) presented a challenge for cryo-EM. Accordingly, we engineered bivalent versions of E2-specific Fabs that doubled the size of Fab-E2 complexes and conferred highly identifiable shapes to the complexes that facilitated particle selection and orientation for image processing. This study validates bivalent Fabs as new fiducial markers for cryo-EM analysis of small proteins such as HCV E2 and identifies a new target epitope for vaccine development.


  • Organizational Affiliation
    • W.M. Keck Laboratory for Structural Biology, University of Maryland-Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CBH-7 Heavy chain
A, C
254Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CBH-7 Light chain
B, D
235Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.935α = 90
b = 101.912β = 100.24
c = 109.936γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 AI132213

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-07-09
    Changes: Database references