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- PDB-8x9w: portal vertex capsomer of the VZV C-Capsid -

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Basic information

Entry
Database: PDB / ID: 8x9w
Titleportal vertex capsomer of the VZV C-Capsid
Components
  • CVC1
  • Capsid vertex component 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Tri1
  • Tri2A
  • Tri2B
  • coiled-coil domain of portal
KeywordsVIRAL PROTEIN / 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 penetration into host nucleus / viral capsid ...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 penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / 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 / 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 ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / 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
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsNan, W. / Lei, C. / Jiangxi, 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 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: coiled-coil domain of portal
C: Major capsid protein
F: Tri2A
H: coiled-coil domain of portal
I: coiled-coil domain of portal
J: coiled-coil domain of portal
K: coiled-coil domain of portal
L: coiled-coil domain of portal
O: Tri2B
Q: coiled-coil domain of portal
R: coiled-coil domain of portal
S: coiled-coil domain of portal
T: coiled-coil domain of portal
X: Tri1
k: CVC1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase


Theoretical massNumber of molelcules
Total (without water)572,91620
Polymers572,91620
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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Protein , 7 types, 18 molecules ACBHIJKLQRSTFOXklm

#1: Protein Major capsid protein / MCP


Mass: 153965.938 Da / Num. of mol.: 2
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
coiled-coil domain of portal


Mass: 7422.140 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#3: Protein Tri2A


Mass: 32225.578 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)
#4: Protein Tri2B


Mass: 33420.516 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)
#5: Protein Tri1


Mass: 32583.186 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)
#6: 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)
#7: Protein Capsid vertex component 2


Mass: 10890.343 Da / Num. of mol.: 2
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: all / 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 Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
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 softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28556 / Symmetry type: POINT
RefinementHighest resolution: 4.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00441780
ELECTRON MICROSCOPYf_angle_d0.82457073
ELECTRON MICROSCOPYf_dihedral_angle_d5.4246079
ELECTRON MICROSCOPYf_chiral_restr0.0456742
ELECTRON MICROSCOPYf_plane_restr0.0067520

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