Biological Assembly 1  

 3D View: Structure

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 3060-mer - A960B900C600D300E120F120G60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 3060-mer - A960B900C600D300E120F60G60H60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 4032.16 kDa 
• Atom Count: 218714 
• Residue Count: 28735 
• Unique protein chains: 7

5ZZ8

Structure of the Herpes simplex virus type 2 C-capsid with capsid-vertex-specific component

• DOI: 10.2210/pdb5ZZ8/pdb
• EMDataResource: EMD-6976

• Classification: STRUCTURAL PROTEIN
• Organism(s): Human alphaherpesvirus 2
• Expression System: Chlorocebus sabaeus
• Mutation(s): No 


• Deposited: 2018-05-31 Released: 2018-10-10 
• Deposition Author(s): Wang, J.L., Yuan, S., Zhu, D.J., Tang, H., Wang, N., Chen, W.Y., Gao, Q., Li, Y.H., Wang, J.Z., Liu, H.R., Zhang, X.Z., Rao, Z.H., Wang, X.X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component.

Wang, J., Yuan, S., Zhu, D., Tang, H., Wang, N., Chen, W., Gao, Q., Li, Y., Wang, J., Liu, H., Zhang, X., Rao, Z., Wang, X.

(2018) Nat Commun 9: 3668-3668

• PubMed: 30201968 
• DOI: 10.1038/s41467-018-06078-4
• Primary Citation of Related Structures:  
  5ZZ8


• PubMed Abstract: 
  

Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α-herpesvirinae subfamily that together with the β- and γ-herpesvirinae subfamilies forms the Herpesviridae family. Here, we report the cryo-electron microscopy structure of the HSV-2 C-capsid with capsid-vertex-specific component (CVSC) that was determined at 3.75 Å using a block-based reconstruction strategy. We present atomic models of multiple conformers for the capsid proteins (VP5, VP23, VP19C, and VP26) and CVSC. Comparison of the HSV-2 homologs yields information about structural similarities and differences between the three herpesviruses sub-families and we identify α-herpesvirus-specific structural features. The hetero-pentameric CVSC, consisting of a UL17 monomer, a UL25 dimer and a UL36 dimer, is bound tightly by a five-helix bundle that forms extensive networks of subunit contacts with surrounding capsid proteins, which reinforce capsid stability.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP19C	1, Q, T, W, w	466	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL38, TRX1
Find proteins for G9I260 (Human herpesvirus 2) Explore G9I260  Go to UniProtKB:  G9I260

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP23	2, 3, R, S, U, V, X, Y, x, y	318	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: TRX2, UL18
Find proteins for P89441 (Human herpesvirus 2 (strain HG52)) Explore P89441  Go to UniProtKB:  P89441

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	1374	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL19, MCP
Find proteins for A0A0E3U2U0 (Human herpesvirus 2) Explore A0A0E3U2U0  Go to UniProtKB:  A0A0E3U2U0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP26	b, c, d, e, f, g, h, i, j, k, l, m, n, o, p	112	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: SCP, UL35
Find proteins for P89458 (Human herpesvirus 2 (strain HG52)) Explore P89458  Go to UniProtKB:  P89458

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
UL17	q	702	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL17, CVC1, HSV2S333_G19
Find proteins for G9I238 (Human herpesvirus 2) Explore G9I238  Go to UniProtKB:  G9I238

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
UL25	r, s	585	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL25, CVC2, HSV2S333_G28
Find proteins for D6PUY5 (Human herpesvirus 2) Explore D6PUY5  Go to UniProtKB:  D6PUY5

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
UL36	t, u	3122	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL36 EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt)
Find proteins for A0A1U9ZLV0 (Human herpesvirus 2) Explore A0A1U9ZLV0  Go to UniProtKB:  A0A1U9ZLV0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-05-31 
• Released Date: 2018-10-10 
Deposition Author(s): Wang, J.L., Yuan, S., Zhu, D.J., Tang, H., Wang, N., Chen, W.Y., Gao, Q., Li, Y.H., Wang, J.Z., Liu, H.R., Zhang, X.Z., Rao, Z.H., Wang, X.X.

Revision History 

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary