6BKD

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D

• PDB DOI: https://doi.org/10.2210/pdb6BKD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Recombinant Hepatitis C virus HK6a/JFH-1, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-11-08 Released: 2018-12-26 
• Deposition Author(s): Tzarum, N., Wilson, I.A., Law, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.286 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.64 kDa 
• Atom Count: 4,440 
• Modelled Residue Count: 580 
• Deposited Residue Count: 635 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A [auth E]	189	Recombinant Hepatitis C virus HK6a/JFH-1	Mutation(s): 1
UniProt
Find proteins for B9V0E2 (Recombinant Hepatitis C virus HK6a/JFH-1) Explore B9V0E2  Go to UniProtKB:  B9V0E2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab AR3D heavy chain	B [auth H]	234	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B2A6 (Homo sapiens) Explore S6B2A6  Go to UniProtKB:  S6B2A6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab AR3D light chain	C [auth L]	212	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6PIL8 (Homo sapiens) Explore Q6PIL8  Go to UniProtKB:  Q6PIL8

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.286 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.318	α = 90
b = 60.392	β = 88
c = 148.082	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
Blu-Ice	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Tzarum, N., Wilson, I.A., Law, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Al123365
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Al106005

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-03-23
  Changes: Author supporting evidence, Database references, Structure summary
• Version 2.2: 2023-10-04
  Changes: Data collection, Refinement description