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- PDB-8x9y: E-hexon capsomer of the VZV C-Capsid -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8x9y
TitleE-hexon capsomer of the VZV C-Capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Tri1
  • Tri2A
  • Tri2B
KeywordsVIRAL PROTEIN / VZV / capsid structure
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral process / viral capsid / host cell nucleus / structural molecule activity
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Major capsid protein / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 1.0Apr 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
Z: Tri1
E: Tri1
A: Small capsomere-interacting protein
B: Major capsid protein
C: Major capsid protein
G: Small capsomere-interacting protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
M: Small capsomere-interacting protein
S: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
k: Small capsomere-interacting protein
L: Tri2A
R: Tri2A
O: Tri2B
V: Tri2B


Theoretical massNumber of molelcules
Total (without water)1,173,17218
Polymers1,173,17218
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 Tri1


Mass: 42776.746 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)
#2: 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
#3: Protein
Major capsid protein / MCP


Mass: 152267.125 Da / Num. of mol.: 6
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
#4: 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)
#5: Protein Tri2B


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)
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: #2-#5, #1 / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1796810 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00581534
ELECTRON MICROSCOPYf_angle_d0.935111180
ELECTRON MICROSCOPYf_dihedral_angle_d5.31811354
ELECTRON MICROSCOPYf_chiral_restr0.05512816
ELECTRON MICROSCOPYf_plane_restr0.00714538

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