8X9W | pdb_00008x9w

portal vertex capsomer of the VZV C-Capsid

• PDB DOI: https://doi.org/10.2210/pdb8X9W/pdb
• EM Map EMD-38186: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• 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., Jiangxi, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 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 20-mer - A10B2C2D2E2F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer - A5B5C2D2E1F1G1H1I1J1 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 572.92 kDa 
• Atom Count: 37,344 
• Modeled Residue Count: 5,160 
• Deposited Residue Count: 5,369 
• Unique protein chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, C	1,387	Human alphaherpesvirus 3	Mutation(s): 0  Gene Names: MCP, 40
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
coiled-coil domain of portal	B, E [auth H], F [auth I], G [auth J], H [auth K], I [auth L], K [auth Q], L [auth R], M [auth S], N [auth T]	87	Human alphaherpesvirus 3	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2A	D [auth F]	297	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	J [auth O]	307	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	O [auth X]	289	Human alphaherpesvirus 3	Mutation(s): 0
UniProt
Find proteins for P09276 (Varicella-zoster virus (strain Dumas)) Explore P09276  Go to UniProtKB:  P09276

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CVC1	P [auth k]	550	Human alphaherpesvirus 3	Mutation(s): 0
UniProt
Find proteins for P10201 (Human herpesvirus 1 (strain 17)) Explore P10201  Go to UniProtKB:  P10201

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 2	Q [auth l], R [auth m]	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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large tegument protein deneddylase	S [auth n], T [auth o]	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 I1UYK0 (Human herpesvirus 1) Explore I1UYK0  Go to UniProtKB:  I1UYK0

Small Molecules

Non-standard Monomers  1 Unique
ID	Chains	Type	Formula	2D Diagram
UNK	B, E [auth H], F [auth I], G [auth J], H [auth K], I [auth L], K [auth Q], L [auth R], M [auth S], N [auth T]	L-PEPTIDE LINKING	C4 H9 N O2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Nan, W., Lei, C., Jiangxi, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection