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- PDB-9jzq: The glycoprotein E of Varicella-Zoster Virus in complex with WLL-... -

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Basic information

Entry
Database: PDB / ID: 9jzq
TitleThe glycoprotein E of Varicella-Zoster Virus in complex with WLL-1/WLL-28 Fab
Components
  • Envelope glycoprotein E
  • WLL-1 Fab heavy chain
  • WLL-1 Fab light chain
  • WLL-28 Fab heavy chain
  • WLL-28 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VZV / glycoprotein E / single B cell / monoclonal antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell junction / host cell Golgi membrane / host cell endosome membrane / entry receptor-mediated virion attachment to host cell / viral envelope / symbiont entry into host cell / virion membrane / enzyme binding / membrane
Similarity search - Function
Envelope glycoprotein E, Fc-binding domain / Envelope glycoprotein E, N-terminal / Alphaherpesvirus glycoprotein E / Alphaherpesvirus glycoprotein E N-terminal / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein E
Similarity search - Component
Biological speciesVaricella-zoster virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWang, L. / Zhang, N. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2025
Title: Discovery and structural investigation of Varicella-Zoster virus gE-neutralizing antibodies isolated from a convalescent patient.
Authors: Lulu Wang / Zihan Jia / Xiaohan Ye / Chunxiao Chen / Baofa Sun / Xiangshuai Zhao / Ruiqi Zhang / Ying Li / Wenya Wang / Zixian Sun / Lushuai Zhou / Zhiyu Ni / Nan Zhang / Yu Guo /
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope glycoprotein E
A: WLL-1 Fab heavy chain
B: WLL-1 Fab light chain
C: WLL-28 Fab heavy chain
D: WLL-28 Fab light chain


Theoretical massNumber of molelcules
Total (without water)157,5485
Polymers157,5485
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Envelope glycoprotein E / gE


Mass: 63171.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Varicella-zoster virus (strain Oka vaccine)
Gene: gE, ORF68 / Production host: Homo sapiens (human) / References: UniProt: Q9J3M8
#2: Antibody WLL-1 Fab heavy chain


Mass: 24313.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody WLL-1 Fab light chain


Mass: 22816.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody WLL-28 Fab heavy chain


Mass: 23929.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody WLL-28 Fab light chain


Mass: 23316.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 and WLL-28
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: YES
Source (natural)Organism: Varicella-zoster virus (strain Oka vaccine)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 324054 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038082
ELECTRON MICROSCOPYf_angle_d0.57311023
ELECTRON MICROSCOPYf_dihedral_angle_d4.9711103
ELECTRON MICROSCOPYf_chiral_restr0.0431253
ELECTRON MICROSCOPYf_plane_restr0.0061412

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