1F8V

THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history. 


Literature

The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA.

Tang, L., Johnson, K.N., Ball, L.A., Lin, T., Yeager, M., Johnson, J.E.

(2001) Nat Struct Biol 8: 77-83

  • DOI: 10.1038/83089
  • Primary Citation of Related Structures:  
    1F8V

  • PubMed Abstract: 

    • The 3.0 A resolution crystal structure of Pariacoto virus (PaV) reveals extensive interactions between portions of the viral RNA genome and the icosahedral capsid. Under the protein shell of the T = 3 quasi equivalent capsid lies a dodecahedral cage composed of RNA duplex that accounts for approximately 35% of the single-stranded RNA genome ...

    The 3.0 A resolution crystal structure of Pariacoto virus (PaV) reveals extensive interactions between portions of the viral RNA genome and the icosahedral capsid. Under the protein shell of the T = 3 quasi equivalent capsid lies a dodecahedral cage composed of RNA duplex that accounts for approximately 35% of the single-stranded RNA genome. The highly basic N-terminal regions (residues 7-54) of the subunits, forming pentamers (A subunits) are clearly visible in the density map and make numerous interactions with the RNA cage. The C-terminal segments (residues 394-401) of the A subunits lie in channels near the quasi three-fold axes. Electron cryo-microscopy and image reconstruction of PaV particles clearly show the dodecahedral RNA cage.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MATURE CAPSID PROTEIN BETAB [auth A],
D [auth B],
F [auth C]		355Pariacoto virusMutation(s): 0 
Gene Names: alpha
EC: 3.4.23.44
UniProt
Find proteins for Q9J7Z0 (Pariacoto virus)
Explore Q9J7Z0 
Go to UniProtKB:  Q9J7Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J7Z0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MATURE CAPSID PROTEIN GAMMAC [auth D],
E,
G [auth F]		40Pariacoto virusMutation(s): 0 
Gene Names: alpha
EC: 3.4.23.44
UniProt
Find proteins for Q9J7Z0 (Pariacoto virus)
Explore Q9J7Z0 
Go to UniProtKB:  Q9J7Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J7Z0
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNAA [auth R]25Pariacoto virus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
H [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 329.332α = 90
b = 346.944β = 90.83
c = 424.893γ = 90
Software Package:
Software NamePurpose
GLRFphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation