5ZZ8

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, 100049, China. xiangxi@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP19CJ [auth 1],
A [auth Q],
D [auth T],
G [auth W],
M [auth w]
466Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: UL38TRX1
UniProt
Find proteins for G9I260 (Human herpesvirus 2)
Explore G9I260 
Go to UniProtKB:  G9I260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9I260
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP23318Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: TRX2UL18
UniProt
Find proteins for P89441 (Human herpesvirus 2 (strain HG52))
Explore P89441 
Go to UniProtKB:  P89441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP89441
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein1,374Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: UL19MCP
UniProt
Find proteins for A0A0E3U2U0 (Human herpesvirus 2)
Explore A0A0E3U2U0 
Go to UniProtKB:  A0A0E3U2U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3U2U0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
VP26112Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: SCPUL35
UniProt
Find proteins for P89458 (Human herpesvirus 2 (strain HG52))
Explore P89458 
Go to UniProtKB:  P89458
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP89458
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
UL17LA [auth q]702Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: UL17CVC1HSV2S333_G19
UniProt
Find proteins for G9I238 (Human herpesvirus 2)
Explore G9I238 
Go to UniProtKB:  G9I238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9I238
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
UL25NA [auth r],
PA [auth s]
585Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: UL25CVC2FKDDOAPL_00028GPADPEBJ_00031HSV2S333_G28
UniProt
Find proteins for D6PUY5 (Human herpesvirus 2)
Explore D6PUY5 
Go to UniProtKB:  D6PUY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6PUY5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UL36RA [auth t],
YA [auth u]
3,122Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: UL36
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt)
UniProt
Find proteins for A0A1U9ZLV0 (Human herpesvirus 2)
Explore A0A1U9ZLV0 
Go to UniProtKB:  A0A1U9ZLV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U9ZLV0
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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