3CJI

Structure of Seneca Valley Virus-001

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus

Venkataraman, S., Reddy, S.P., Loo, J., Idamakanti, N., Hallenbeck, P.L., Reddy, V.S.

(2008) Structure 16: 1555-1561

  • DOI: 10.1016/j.str.2008.07.013
  • Primary Citation of Related Structures:  
    3CJI

  • PubMed Abstract: 

    • The crystal structure of Seneca Valley Virus-001 (SVV-001), the representative member of a new genus, Senecavirus, is reported at 2.3A resolution. SVV-001 is the first naturally occurring nonpathogenic picornavirus shown to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features ...

    The crystal structure of Seneca Valley Virus-001 (SVV-001), the representative member of a new genus, Senecavirus, is reported at 2.3A resolution. SVV-001 is the first naturally occurring nonpathogenic picornavirus shown to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+) ssRNA genome of SVV-001 shares closest sequence similarity with the genomes of the members of Cardiovirus. The overall tertiary structure of VP1-VP4 subunits is conserved with the exception of loops, especially those of VP1 that show large deviations relative to the members of the cardioviruses. The surface loops of VP1 and VP2 are predicted to mediate cell tropism of SVV-001. In addition, the organization of the packaged nucleic acid density indicates that certain regions of VP2 and VP4 interact closely with the packaged nucleic acid.

    Organizational Affiliation: 

    Department of Molecular Biology, TPC-6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinA263Senecavirus AMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.19.12 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
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Go to UniProtKB:  Q155Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ155Z9
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinB239Senecavirus AMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.19.12 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Explore Q155Z9 
Go to UniProtKB:  Q155Z9
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ155Z9
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinC284Senecavirus AMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.19.12 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Explore Q155Z9 
Go to UniProtKB:  Q155Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ155Z9
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinD71Senecavirus AMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.19.12 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Explore Q155Z9 
Go to UniProtKB:  Q155Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ155Z9
Protein Feature View
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 311.51α = 90
b = 311.51β = 90
c = 1526.401γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance