5ZAP

Atomic structure of the herpes simplex virus type 2 B-capsid


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 1.2 of the entry. See complete history


Literature

Cryo-EM structure of a herpesvirus capsid at 3.1 angstrom.

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

(2018) Science 360

  • DOI: https://doi.org/10.1126/science.aao7283
  • Primary Citation of Related Structures:  
    5ZAP

  • PubMed Abstract: 

    Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV.


  • Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein1,374Human alphaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for G9I240 (Human herpesvirus 2)
Explore G9I240 
Go to UniProtKB:  G9I240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9I240
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2318Human alphaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for G9I239 (Human herpesvirus 2)
Explore G9I239 
Go to UniProtKB:  G9I239
Entity Groups  
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UniProt GroupG9I239
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1BA [auth b],
EA [auth e],
S,
V,
Y
466Human alphaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for A0A1U9ZFW1 (Human herpesvirus 2)
Explore A0A1U9ZFW1 
Go to UniProtKB:  A0A1U9ZFW1
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UniProt GroupA0A1U9ZFW1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting protein112Human alphaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for G9I257 (Human herpesvirus 2)
Explore G9I257 
Go to UniProtKB:  G9I257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9I257
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-05
    Changes: Data collection, Structure summary