1HI0

RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus initiation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    1HI1, 1HI0, 1HI8, 1HHT, 1HHS

  • 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 double-stranded RNA ...

    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 D Biol Crystallogr 56: 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P2 PROTEIND [auth P], E [auth Q], F [auth R]664Pseudomonas virus phi6Mutation(s): 0 
Gene Names: P2
EC: 2.7.7.48
UniProt
Find proteins for P11124 (Pseudomonas phage phi6)
Explore P11124 
Go to UniProtKB:  P11124
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-(*TP*TP*TP*CP*C)-3')A [auth D], B [auth E], C [auth F]5N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GTP
    Query on GTP

    Download Ideal Coordinates CCD File 
    H [auth P], I [auth P], M [auth Q], N [auth Q], R, S [auth R]GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    G [auth P], L [auth Q], Q [auth R]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    J [auth P], K [auth P], O [auth Q], P [auth Q], T [auth R], U [auth R]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.239 
    • R-Value Work: 0.214 
    • R-Value Observed: 0.214 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 105.65α = 90
    b = 92.7β = 101.09
    c = 140.79γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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