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 virusMutation(s): 0 
Gene Names: alpha
Find proteins for Q9J7Z0 (Pariacoto virus)
Go to UniProtKB:  Q9J7Z0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MATURE CAPSID PROTEIN GAMMA
D, E, F
40Pariacoto virusMutation(s): 0 
Gene Names: alpha
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
Download SDF File 
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
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling
GLRFphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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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