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- PDB-9no1: Cryo-ET map of the VZV capsid vertex (5-fold axis). -

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Basic information

Entry
Database: PDB / ID: 9no1
TitleCryo-ET map of the VZV capsid vertex (5-fold axis).
Components
  • Large tegument protein deneddylase
  • ORF20
  • ORF34
  • ORF40
  • ORF41
  • ORF43
  • Small capsomere-interacting protein
KeywordsVIRUS / Varicella-zoster virus / capsid / cryo-ET / cryo-FIB
Function / homology
Function and homology information


deNEDDylase activity / viral genome packaging / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid ...deNEDDylase activity / viral genome packaging / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / 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 capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / DNA polymerase family B signature. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ORF43 / ORF41 / ORF40 / ORF34 / Small capsomere-interacting protein / ORF20 / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.3 Å
AuthorsOliver, S.L. / Chen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Cryogenic Electron Tomography Redefines Herpesvirus Capsid Assembly Intermediates Inside the Cell Nucleus.
Authors: Stefan L Oliver / Muyuan Chen / Leeya Engel / Corey W Hecksel / Xueting Zhou / Michael F Schmid / Ann M Arvin / Wah Chiu
Abstract: Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been ...Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been characterized, but their roles in herpesvirus replication remain controversial. The status of the capsid vertex-specific component (CVSC), essential for capsid stability and dsDNA packaging and retention, is also unclear. By integrating cryogenic focused ion beam milling with electron tomography and subtomogram averaging, we derived atomic models for all protein components, including the CVSC, across different herpesvirus capsid types within infected cell nuclei. Focused classification of pentonal vertex densities revealed differences in CVSC occupancy between genome-filled capsids and capsids lacking dsDNA, highlighting structural heterogeneity and providing insight into distinct capsid assembly stages . These intra-nuclear findings redefine the maturation model of herpesvirus capsid assembly, advancing the understanding of herpesvirus replication, and demonstrate the effectiveness of electron imaging by studying virus assembly within host cells.
History
DepositionMar 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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: ORF40
B: ORF40
C: Small capsomere-interacting protein
D: ORF40
E: Small capsomere-interacting protein
F: ORF40
G: Small capsomere-interacting protein
H: ORF40
I: Small capsomere-interacting protein
J: ORF40
K: Small capsomere-interacting protein
L: ORF40
M: Small capsomere-interacting protein
N: ORF20
O: ORF41
P: ORF41
Q: ORF20
R: ORF41
S: ORF41
T: ORF43
U: ORF34
V: ORF34
W: Large tegument protein deneddylase
X: Large tegument protein deneddylase


Theoretical massNumber of molelcules
Total (without water)2,296,22224
Polymers2,296,22224
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, 24 molecules ABDFHJLCEGIKMNQOPRSTUVWX

#1: Protein
ORF40


Mass: 155145.359 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQT5
#2: Protein
Small capsomere-interacting protein


Mass: 24440.119 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQV2
#3: Protein ORF20


Mass: 54028.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQV5
#4: Protein
ORF41


Mass: 34421.914 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQT4
#5: Protein ORF43


Mass: 73978.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQT2
#6: Protein ORF34


Mass: 65253.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQU1
#7: Protein Large tegument protein deneddylase


Mass: 306666.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Human alphaherpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q4JQX9, 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: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Human alphaherpesvirus 3 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus) / Strain: pOka
Source (recombinant)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus) / Strain: pOka / Cell: MeWo
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 1250 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 0.974 sec. / Electron dose: 1.577 e/Å2 / Avg electron dose per subtomogram: 82.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM softwareName: EMAN2 / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3804 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 69 / Num. of volumes extracted: 3804

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