8XA0 | pdb_00008xa0

penton capsomer of the VZV C-capsid

• PDB DOI: https://doi.org/10.2210/pdb8XA0/pdb
• EM Map EMD-38190: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Human alphaherpesvirus 3
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-12-01 Released: 2024-12-04 
• Deposition Author(s): Nan, W., Lei, C., Xiangxi, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures

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.

(2024) Hlife 2: 64-74

• DOI: https://doi.org/10.1016/j.hlife.2023.10.007

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A5B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 13-mer - A5B2C2D1E1F1G1 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 957.33 kDa 
• Atom Count: 57,027 
• Modeled Residue Count: 7,398 
• Deposited Residue Count: 8,633 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large tegument protein deneddylase	A [auth 2], J [auth y]	47	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: UL36 EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P10220 (Human herpesvirus 1 (strain 17)) Explore P10220  Go to UniProtKB:  P10220

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	B [auth A], C, D [auth E], E [auth F], F [auth G]	1,370	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: ORF40, MCP, ORF 40, HHV3_E_SVETAgp42, HHV3_gp42, HHV3gp42
UniProt
Find proteins for Q6QCL5 (Human herpesvirus 3) Explore Q6QCL5  Go to UniProtKB:  Q6QCL5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 1	G [auth h]	696	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: CVC1, UL17
UniProt
Find proteins for P10201 (Human herpesvirus 1 (strain 17)) Explore P10201  Go to UniProtKB:  P10201

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 2	H [auth q], I [auth u]	94	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: CVC2, UL25
UniProt
Find proteins for P10209 (Human herpesvirus 1 (strain 17)) Explore P10209  Go to UniProtKB:  P10209

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2A	K [auth R]	256	Human alphaherpesvirus 3	Mutation(s): 0
UniProt
Find proteins for P09291 (Varicella-zoster virus (strain Dumas)) Explore P09291  Go to UniProtKB:  P09291

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2B	L [auth V]	263	Human alphaherpesvirus 3	Mutation(s): 0
UniProt
Find proteins for P09291 (Varicella-zoster virus (strain Dumas)) Explore P09291  Go to UniProtKB:  P09291

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri1	M [auth Z]	286	Human alphaherpesvirus 3	Mutation(s): 0
UniProt
Find proteins for P09276 (Varicella-zoster virus (strain Dumas)) Explore P09276  Go to UniProtKB:  P09276

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Nan, W., Lei, C., Xiangxi, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release