7QW9

Cryo-EM structure of coxsackievirus A6 mature virion


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion.

Buttner, C.R.Spurny, R.Fuzik, T.Plevka, P.

(2022) Commun Biol 5: 898-898

  • DOI: https://doi.org/10.1038/s42003-022-03863-2
  • Primary Citation of Related Structures:  
    7QVX, 7QVY, 7QW9

  • PubMed Abstract: 

    Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous structural studies, and it was speculated that the virus is unique among enteroviruses in using altered particles with expanded capsids to infect cells. In contrast, the virions of other enteroviruses are required for infection. Here we used cryo-electron microscopy (cryo-EM) to determine the structures of the CV-A6 virion, altered particle, and empty capsid. We show that the CV-A6 virion has features characteristic of virions of other enteroviruses, including a compact capsid, VP4 attached to the inner capsid surface, and fatty acid-like molecules occupying the hydrophobic pockets in VP1 subunits. Furthermore, we found that in a purified sample of CV-A6, the ratio of infectious units to virions is 1 to 500. Therefore, it is likely that virions of CV-A6 initiate infection, like those of other enteroviruses. Our results provide evidence that future vaccines against CV-A6 should target its virions instead of the antigenically distinct altered particles. Furthermore, the structure of the virion provides the basis for the rational development of capsid-binding inhibitors that block the genome release of CV-A6.


  • Organizational Affiliation

    Central European Institute of Technology - Masaryk University, Structural Biology, Structural Virology, Kamenice 5, 62500, Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1304Coxsackievirus A6Mutation(s): 0 
UniProt
Find proteins for Q6JKS2 (Coxsackievirus A6)
Explore Q6JKS2 
Go to UniProtKB:  Q6JKS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JKS2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2256Coxsackievirus A6Mutation(s): 0 
UniProt
Find proteins for Q6JKS2 (Coxsackievirus A6)
Explore Q6JKS2 
Go to UniProtKB:  Q6JKS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JKS2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3241Coxsackievirus A6Mutation(s): 0 
UniProt
Find proteins for Q6JKS2 (Coxsackievirus A6)
Explore Q6JKS2 
Go to UniProtKB:  Q6JKS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JKS2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP468Coxsackievirus A6Mutation(s): 0 
UniProt
Find proteins for Q6JKS2 (Coxsackievirus A6)
Explore Q6JKS2 
Go to UniProtKB:  Q6JKS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JKS2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.5
MODEL REFINEMENTPHENIX1.19.2
MODEL REFINEMENTREFMAC5
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech RepublicGX-1925982X
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2018127

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Refinement description