8X9Z | pdb_00008x9z

P-hexon capsomer of the VZV C-Capsid

PDB DOI: https://doi.org/10.2210/pdb8X9Z/pdb
EM Map EMD-38189: EMDB EMDataResource

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

Deposited: 2023-12-01 Released: 2025-11-19
Deposition Author(s): Nan, W., Lei, C., Xiangxi, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 1,395.63 kDa
Atom Count: 93,092
Modeled Residue Count: 12,077
Deposited Residue Count: 12,578
Unique protein chains: 11

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, C [auth F], D [auth G], E [auth H], F [auth I]	1,369	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09245
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	B [auth E]	1,370	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09245
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	G [auth J]	1,371	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09245
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small capsomere-interacting protein	H [auth L] I [auth R] J [auth X] K [auth d] L [auth e] H [auth L], I [auth R], J [auth X], K [auth d], L [auth e], M [auth f]	94	Human alphaherpesvirus 3	Mutation(s): 0 Gene Names: SCP
UniProt
Find proteins for U5NQG6 (Human herpesvirus 3) Explore U5NQG6 Go to UniProtKB: U5NQG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5NQG6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CVC1	N [auth k]	550	Human alphaherpesvirus 3	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 2	O [auth l]	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10209
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 2	P [auth m]	80	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10209
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large tegument protein deneddylase	Q [auth n], R [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 P10220 (Human herpesvirus 1 (strain 17)) Explore P10220 Go to UniProtKB: P10220
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10220
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2A	S [auth P], T [auth a]	256	Human alphaherpesvirus 3	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri2A	U [auth V], V [auth b]	263	Human alphaherpesvirus 3	Mutation(s): 0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Tri1	W [auth c], X [auth h]	286	Human alphaherpesvirus 3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence