6BZW | pdb_00006bzw

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody AP33

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.231 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.7 of the entry. See complete history. 

Literature

Immunogenetic and structural analysis of a class of HCV broadly neutralizing antibodies and their precursors.

Aleman, F., Tzarum, N., Kong, L., Nagy, K., Zhu, J., Wilson, I.A., Law, M.

(2018) Proc Natl Acad Sci U S A 115: 7569-7574

  • DOI: https://doi.org/10.1073/pnas.1802378115
  • Primary Citation Related Structures: 
    6BZU, 6BZV, 6BZW, 6BZY

  • PubMed Abstract: 

    Elicitation of broadly neutralizing antibodies (bnAbs) is a leading strategy in rational vaccine design against antigenically diverse pathogens. Here, we studied a panel of monoclonal antibodies (mAbs) from mice immunized with the hepatitis C virus (HCV) envelope glycoproteins E1E2. Six of the mAbs recognize the conserved E2 antigenic site 412-423 (AS412) and cross-neutralize diverse HCV genotypes. Immunogenetic and structural analysis revealed that the antibodies originated from two different germline (GL) precursors and bind AS412 in a β-hairpin conformation. Intriguingly, the anti-HCV activity of one antibody lineage is associated with maturation of the light chain (LC), whereas the other lineage is dependent on heavy-chain (HC) maturation. Crystal structures of GL precursors of the LC-dependent lineage in complex with AS412 offer critical insights into the maturation process of bnAbs to HCV, providing a scientific foundation for utilizing the mouse model to study AS412-targeting vaccine candidates.

    • Organizational Affiliation: 
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecule Content 

  • Total Structure Weight: 197.57 kDa 
  • Atom Count: 14,240 
  • Modeled Residue Count: 1,780 
  • Deposited Residue Count: 1,820 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP33 GL Heavy ChainA [auth C],
C [auth A],
E,
G		223Mus musculusMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AP33 GL Light ChainB [auth D],
D [auth B],
F,
H		219Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
E2 AS412 peptide
I, J, K, L
13Orthohepacivirus 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.231 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.356α = 90
b = 84.709β = 89.96
c = 192.919γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI106005
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123365

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.5: 2022-02-02
    Changes: Database references, Structure summary
  • Version 1.6: 2023-10-04
    Changes: Data collection, Refinement description
  • Version 1.7: 2024-10-23
    Changes: Structure summary