1HI8

RNA dependent RNA polymerase from dsRNA bacteriophage phi6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Mechanism for Initiating RNA-Dependent RNA Polymerization

Butcher, S.J.Grimes, J.M.Makeyev, E.V.Bamford, D.H.Stuart, D.I.

(2001) Nature 410: 235

  • DOI: 10.1038/35065653
  • Primary Citation of Related Structures:  1HHS, 1HHT, 1HI0, 1HI1

  • PubMed Abstract: 
  • In most RNA viruses, genome replication and transcription are catalysed by a viral RNA-dependent RNA polymerase. Double-stranded RNA viruses perform these operations in a capsid (the polymerase complex), using an enzyme that can read both single- and ...

    In most RNA viruses, genome replication and transcription are catalysed by a viral RNA-dependent RNA polymerase. Double-stranded RNA viruses perform these operations in a capsid (the polymerase complex), using an enzyme that can read both single- and double-stranded RNA. Structures have been solved for such viral capsids, but they do not resolve the polymerase subunits in any detail. Here we show that the 2 A resolution X-ray structure of the active polymerase subunit from the double-stranded RNA bacteriophage straight phi6 is highly similar to that of the polymerase of hepatitis C virus, providing an evolutionary link between double-stranded RNA viruses and flaviviruses. By crystal soaking and co-crystallization, we determined a number of other structures, including complexes with oligonucleotide and/or nucleoside triphosphates (NTPs), that suggest a mechanism by which the incoming double-stranded RNA is opened up to feed the template through to the active site, while the substrates enter by another route. The template strand initially overshoots, locking into a specificity pocket, and then, in the presence of cognate NTPs, reverses to form the initiation complex; this process engages two NTPs, one of which acts with the carboxy-terminal domain of the protein to prime the reaction. Our results provide a working model for the initiation of replication and transcription.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Studies on the Bacteriophage Phi6 RNA-Dependent RNA Polymerase
      Butcher, S.J.,Makeyev, E.V.,Grimes, J.M.,Stuart, D.I.,Bamford, D.H.
      (2000) Acta Crystallogr.,Sect.D D56: 1473


    Organizational Affiliation

    Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, PO Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P2 PROTEIN
A, B
664Pseudomonas phage phi6Gene Names: P2
EC: 2.7.7.48
Find proteins for P11124 (Pseudomonas phage phi6)
Go to UniProtKB:  P11124
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.280 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 110.000α = 90.00
b = 110.000β = 90.00
c = 159.300γ = 120.00
Software Package:
Software NamePurpose
SnBphasing
CNSrefinement
SCALEPACKdata scaling
SHARPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Refinement description