6BKC | pdb_00006bkc

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.276 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6BKC

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Genetic and structural insights into broad neutralization of hepatitis C virus by human VH1-69 antibodies.

Tzarum, N.Giang, E.Kong, L.He, L.Prentoe, J.Augestad, E.Hua, Y.Castillo, S.Lauer, G.M.Bukh, J.Zhu, J.Wilson, I.A.Law, M.

(2019) Sci Adv 5: eaav1882-eaav1882

  • DOI: https://doi.org/10.1126/sciadv.aav1882
  • Primary Citation Related Structures: 
    6BKB, 6BKC, 6BKD

  • PubMed Abstract: 

    An effective vaccine to the antigenically diverse hepatitis C virus (HCV) must target conserved immune epitopes. Here, we investigate cross-neutralization of HCV genotypes by broadly neutralizing antibodies (bNAbs) encoded by the relatively abundant human gene family V H 1-69 . We have deciphered the molecular requirements for cross-neutralization by this unique class of human antibodies from crystal structures of HCV E2 in complex with bNAbs. An unusually high binding affinity is found for germ line-reverted versions of V H 1-69 precursor antibodies, and neutralization breadth is acquired during affinity maturation. Deep sequencing analysis of an HCV-immune B cell repertoire further demonstrates the importance of the V H 1-69 gene family in the generation of HCV bNAbs. This study therefore provides critical insights into immune recognition of HCV with important implications for rational vaccine design.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 69.05 kDa 
  • Atom Count: 4,473 
  • Modeled Residue Count: 576 
  • Deposited Residue Count: 634 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab AR3B heavy chainA [auth H]230Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab AR3B light chainB [auth L]215Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCD0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PolyproteinC [auth E]189Recombinant Hepatitis C virus HK6a/JFH-1Mutation(s): 1 
UniProt
Find proteins for B9V0E2 (Recombinant Hepatitis C virus HK6a/JFH-1)
Explore B9V0E2 
Go to UniProtKB:  B9V0E2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9V0E2
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.276 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.447α = 90
b = 59.437β = 90.29
c = 143.923γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAl123365
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAl106005

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Structure summary