1F8V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


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.Mol.Biol. 8: 77-83

  • DOI: 10.1038/83089

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MATURE CAPSID PROTEIN BETA
A, B, C
355Pariacoto virusGene Names: alpha
EC: 3.4.23.44
Find proteins for Q9J7Z0 (Pariacoto virus)
Go to UniProtKB:  Q9J7Z0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MATURE CAPSID PROTEIN GAMMA
D, E, F
40Pariacoto virusGene Names: alpha
EC: 3.4.23.44
Find proteins for Q9J7Z0 (Pariacoto virus)
Go to UniProtKB:  Q9J7Z0
Entity ID: 1
MoleculeChainsLengthOrganism
RNAR25Pariacoto virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 329.332α = 90.00
b = 346.944β = 90.83
c = 424.893γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
GLRFphasing
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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