8X9X | pdb_00008x9x

C-hexon capsomer of the VZV C-Capsid

• PDB DOI: https://doi.org/10.2210/pdb8X9X/pdb
• EM Map EMD-38187: EMDB EMDataResource

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


• Deposited: 2023-12-01 Released: 2025-04-30 
• 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: 3.10 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 18-mer - A6B6C4D2 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - A6B6 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,155 kDa 
• Atom Count: 78,435 
• Modeled Residue Count: 10,200 
• Deposited Residue Count: 10,428 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, C, D, E, F, H	1,369	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: ORF40, MCP, ORF 40, HHV3_E_SVETAgp42, HHV3_gp42, HHV3gp42
UniProt
Find proteins for P09245 (Varicella-zoster virus (strain Dumas)) Explore P09245  Go to UniProtKB:  P09245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small capsomere-interacting protein	B, G, I [auth L], J [auth Q], K [auth V], L [auth g]	94	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: SCP
UniProt
Find proteins for P09279 (Varicella-zoster virus (strain Dumas)) Explore P09279  Go to UniProtKB:  P09279

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2A	M [auth I], N [auth K]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2B	O [auth N], P	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri1	Q [auth S], R [auth U]	306	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: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
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: 2025-04-30
  Type: Initial release