6UYG

Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 core from genotype 6a bound to broadly neutralizing antibody AR3A and non neutralizing antibody E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

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This is version 2.1 of the entry. See complete history


Literature

Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines.

He, L.Tzarum, N.Lin, X.Shapero, B.Sou, C.Mann, C.J.Stano, A.Zhang, L.Nagy, K.Giang, E.Law, M.Wilson, I.A.Zhu, J.

(2020) Sci Adv 6: eaaz6225-eaaz6225

  • DOI: 10.1126/sciadv.aaz6225
  • Primary Citation of Related Structures:  
    6UYD, 6UYF, 6UYG, 6UYM

  • PubMed Abstract: 
  • Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are responsible for cell entry, with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell-based HCV vaccine development through E2 optimization and nanoparticle display ...

    Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are responsible for cell entry, with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell-based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved substantial yield and purity, as well as enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B cell patterns associated with nanoparticle-induced antibody responses, which target the conserved neutralizing epitopes on E2 and cross-neutralize HCV genotypes.


    Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein E2A [auth E]189Recombinant Hepatitis C virus HK6a/JFH-1Mutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for B9V0E2 (Recombinant Hepatitis C virus HK6a/JFH-1)
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Go to UniProtKB:  B9V0E2
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UniProt GroupB9V0E2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab AR3A heavy chainB [auth H]232Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab AR3A light chainC [auth L]214Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab E1 heavy chainD [auth A]227Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Fab E1 light chainE [auth B]219Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein GF [auth G]61Streptococcus sp.Mutation(s): 0 
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Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
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Oligosaccharides

Help

Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth E],
I [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.824α = 90
b = 209.824β = 90
c = 139.942γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection

Structure Validation

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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 StatesAI124337
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI129698
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123861
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI079031
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123365
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI106005

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: 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: 2021-03-10
    Changes: Structure summary