3CJI

Structure of Seneca Valley Virus-001

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


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

  • 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 cytotoxi ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
A
263Seneca Valley virus (isolate -/United States/SSV-001/2002)Mutation(s): 0 
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Go to UniProtKB:  Q155Z9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
B
239Seneca Valley virus (isolate -/United States/SSV-001/2002)Mutation(s): 0 
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Go to UniProtKB:  Q155Z9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
C
284Seneca Valley virus (isolate -/United States/SSV-001/2002)Mutation(s): 0 
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Go to UniProtKB:  Q155Z9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
D
71Seneca Valley virus (isolate -/United States/SSV-001/2002)Mutation(s): 0 
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
Go to UniProtKB:  Q155Z9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.258 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 311.510α = 90.00
b = 311.510β = 90.00
c = 1526.400γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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