8CXP

Characterisation of a Seneca Valley Virus Thermostable Mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Characterisation of a Seneca Valley virus thermostable mutant.

Jayawardena, N.McCarthy, C.Wang, I.Waqqar, S.Burga, L.N.Strauss, M.Bostina, M.

(2022) Virology 575: 74-82

  • DOI: https://doi.org/10.1016/j.virol.2022.08.015
  • Primary Citation of Related Structures:  
    8CXP

  • PubMed Abstract: 

    Seneca Valley virus (SVV) is a newly discovered picornavirus in the Senecavirus genus. SVV-001 strain has shown promise as an oncolytic virus against tumors with neuroendocrine features. There is a need to use a structure-based approach to develop virus-like particles capable to mimicking the architecture of naturally occurring empty capsids that can be used as vaccines or as carriers for targeted cancer treatment. However, these empty capsids are inherently less stable, and tedious to purify. This warrants investigation into factors which confer the SVV capsid stability and into combining this knowledge to recombinantly express stable SVV VLPs. In this study, we isolated a thermostable mutant of SVV by thermal selection assays and we characterized a single mutation located in a capsid protein. The cryo-EM map of this mutant showed conformational shifts that facilitated the formation of additional hydrogen bonds and aromatic interactions, which could serve as capsid stabilizing factors.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1263Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A649YC68 (Senecavirus A)
Explore A0A649YC68 
Go to UniProtKB:  A0A649YC68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A649YC68
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3239Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A649YC94 (Senecavirus A)
Explore A0A649YC94 
Go to UniProtKB:  A0A649YC94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A649YC94
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP2284Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A1U9IRU2 (Senecavirus A)
Explore A0A1U9IRU2 
Go to UniProtKB:  A0A1U9IRU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U9IRU2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP471Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A649YCC5 (Senecavirus A)
Explore A0A649YCC5 
Go to UniProtKB:  A0A649YCC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A649YCC5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release