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- PDB-8x9z: P-hexon capsomer of the VZV C-Capsid -

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Basic information

Entry
Database: PDB / ID: 8x9z
TitleP-hexon capsomer of the VZV C-Capsid
Components
  • (Capsid vertex component ...) x 2
  • (Major capsid ...) x 3
  • (Tri2A) x 2
  • CVC1
  • Large tegument protein deneddylase
  • Small capsomere-interacting protein
  • Tri1
KeywordsVIRUS / VZV / capsid structure
Function / homology
Function and homology information


nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral process / viral penetration into host nucleus ...nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral process / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNan, W. / Lei, C. / Xiangxi, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2024
Title: Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures
Authors: Cao, L. / Wang, N. / Lv, Z. / Chen, W. / Chen, Z. / Song, L. / Sha, X. / Wang, G. / Hu, Y. / Lian, X. / Cui, G. / Fan, J. / Quan, Y. / Liu, H. / Hou, H. / Wang, X.
History
DepositionDec 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
L: Small capsomere-interacting protein
R: Small capsomere-interacting protein
X: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Small capsomere-interacting protein
k: CVC1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase
P: Tri2A
a: Tri2A
V: Tri2A
b: Tri2A
c: Tri1
h: Tri1


Theoretical massNumber of molelcules
Total (without water)1,395,63524
Polymers1,395,63524
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

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Major capsid ... , 3 types, 7 molecules AFGHIEJ

#1: Protein
Major capsid protein / MCP


Mass: 152267.125 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: MCP, 40 / Production host: Homo sapiens (human) / References: UniProt: P09245
#2: Protein Major capsid protein / MCP


Mass: 152354.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: MCP, 40 / Production host: Homo sapiens (human) / References: UniProt: P09245
#3: Protein Major capsid protein / MCP


Mass: 152468.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: MCP, 40 / Production host: Homo sapiens (human) / References: UniProt: P09245

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Protein , 5 types, 13 molecules LRXdefkPaVbch

#4: Protein
Small capsomere-interacting protein


Mass: 10185.611 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: SCP / Production host: Homo sapiens (human) / References: UniProt: U5NQG6
#5: Protein CVC1


Mass: 59751.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#9: Protein Tri2A


Mass: 27729.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#10: Protein Tri2A


Mass: 28721.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#11: Protein Tri1


Mass: 32268.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)

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Capsid vertex component ... , 2 types, 2 molecules lm

#6: Protein Capsid vertex component 2


Mass: 10890.343 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: CVC2, UL25 / Production host: Homo sapiens (human) / References: UniProt: P10209
#7: Protein Capsid vertex component 2


Mass: 9280.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: CVC2, UL25 / Production host: Homo sapiens (human) / References: UniProt: P10209

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Protein/peptide , 1 types, 2 molecules no

#8: Protein/peptide Large tegument protein deneddylase


Mass: 5500.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: UL36 / Production host: Homo sapiens (human)
References: UniProt: P10220, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Details

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: Human alphaherpesvirus 3 / Type: VIRUS / Entity ID: #10-#11, #1-#9 / Source: NATURAL
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1671456 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00595364
ELECTRON MICROSCOPYf_angle_d1.063129977
ELECTRON MICROSCOPYf_dihedral_angle_d5.92813258
ELECTRON MICROSCOPYf_chiral_restr0.05614920
ELECTRON MICROSCOPYf_plane_restr0.00816988

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