8V5L | pdb_00008v5l

Structure of the Varicella Zoster Virus (VZV) gI binding domain of glycoprotein E (gE) in complex with human Fab 1A2 and 1E12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 
    0.269 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structures of the Varicella Zoster Virus Glycoprotein E and Epitope Mapping of Vaccine-Elicited Antibodies.

Harshbarger, W.D.Holzapfel, G.Seraj, N.Tian, S.Chesterman, C.Fu, Z.Pan, Y.Harelson, C.Peng, D.Huang, Y.Chandramouli, S.Malito, E.Bottomley, M.J.Williams, J.

(2024) Vaccines (Basel) 12

  • DOI: https://doi.org/10.3390/vaccines12101111
  • Primary Citation Related Structures: 
    8V5L, 8V5P, 8V5Q, 8V5S

  • PubMed Abstract: 

    Background: Varicella zoster virus (VZV) is the causative agent for chickenpox and herpes zoster (HZ, shingles). HZ is a debilitating disease affecting elderly and immunocompromised populations. Glycoprotein E (gE) is indispensable for viral replication and cell-to-cell spread and is the primary target for anti-VZV antibodies. Importantly, gE is the sole antigen in Shingrix, a highly efficacious, AS01 B -adjuvanted vaccine approved in multiple countries for the prevention of HZ, yet the three-dimensional (3D) structure of gE remains elusive. Objectives : We sought to determine the structure of VZV gE and to understand in detail its interactions with neutralizing antibodies. Methods : We used X-ray crystallography and cryo-electron microscopy to elucidate structures of gE bound by recombinant Fabs of antibodies previously elicited through vaccination with Zostavax, a live, attenuated vaccine. Results : The 3D structures resolve distinct central and C-terminal antigenic domains, presenting an array of diverse conformational epitopes. The central domain has two beta-sheets and two alpha helices, including an IgG-like fold. The C-terminal domain exhibits 3 beta-sheets and an Ig-like fold and high structural similarity to HSV1 gE. Conclusions : gE from VZV-infected cells elicits a human antibody response with a preference for the gI binding domain of gE. These results yield insights to VZV gE structure and immunogenicity, provide a framework for future studies, and may guide the design of additional herpesvirus vaccine antigens. Teaser: Structures of varicella zoster virus glycoprotein E reveal distinct antigenic domains and define epitopes for vaccine-elicited human antibodies.


  • Organizational Affiliation
    • GSK, Rockville, MD 20850, USA.

Macromolecule Content 

  • Total Structure Weight: 123.59 kDa 
  • Atom Count: 7,752 
  • Modeled Residue Count: 1,010 
  • Deposited Residue Count: 1,127 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1A2 Heavy ChainA [auth H]243Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1A2 Light ChainB [auth L]214Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein EC [auth A]203Human alphaherpesvirus 3Mutation(s): 0 
UniProt
Find proteins for A6XEF7 (Human herpesvirus 3)
Explore A6XEF7 
Go to UniProtKB:  A6XEF7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6XEF7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1E12 Heavy ChainD [auth B]248Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1E12 Light ChainE [auth C]219Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.269 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.776α = 90
b = 63.493β = 99.96
c = 96.484γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
autoPROCdata reduction
PHASERphasing
autoPROCdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references