4F5X

Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.293 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Location of the dsRNA-Dependent Polymerase, VP1, in Rotavirus Particles.

Estrozi, L.F.Settembre, E.C.Goret, G.McClain, B.Zhang, X.Chen, J.Z.Grigorieff, N.Harrison, S.C.

(2013) J.Mol.Biol. 425: 124-132

  • DOI: 10.1016/j.jmb.2012.10.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-lay ...

    Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, Grenoble 38042, France. estrozi@embl.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP2 protein
A, B
880Bovine rotavirus AMutation(s): 0 
Find proteins for H9N1A6 (Bovine rotavirus A)
Go to UniProtKB:  H9N1A6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Intermediate capsid protein VP6
C, D, E, F, G, H, I, J, K, L, M, N, O
397Rotavirus A (strain RVA/Cow/United States/NCDV-Lincoln/1969/G6P6[1])Mutation(s): 0 
Find proteins for A7J3A1 (Rotavirus A (strain RVA/Cow/United States/NCDV-Lincoln/1969/G6P6[1]))
Go to UniProtKB:  A7J3A1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
W
1089Rotavirus A (strain RVA/SA11-Patton/G3P[X])Mutation(s): 0 
EC: 2.7.7.48
Find proteins for O37061 (Rotavirus A (strain RVA/SA11-Patton/G3P[X]))
Go to UniProtKB:  O37061
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, F, I, L, O
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.293 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 740.750α = 90.00
b = 1198.070β = 90.00
c = 1345.410γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
CNSphasing
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references
  • Version 1.2: 2013-01-16
    Type: Database references