3AVX

Structure of viral RNA polymerase complex 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for RNA polymerization by Q beta replicase

Takeshita, D.Tomita, K.

(2012) Nat Struct Mol Biol 19: 229-237

  • DOI: 10.1038/nsmb.2204
  • Primary Citation of Related Structures:  
    3AVX, 3AVY, 3AVT, 3AVU, 3AVV, 3AVW

  • PubMed Abstract: 
  • Core Qβ replicase comprises the Qβ virus-encoded RNA-dependent RNA polymerase (β-subunit) and the host Escherichia coli translational elongation factors EF-Tu and EF-Ts. The functions of the host proteins in the viral replicase are not clear. Structu ...

    Core Qβ replicase comprises the Qβ virus-encoded RNA-dependent RNA polymerase (β-subunit) and the host Escherichia coli translational elongation factors EF-Tu and EF-Ts. The functions of the host proteins in the viral replicase are not clear. Structural analyses of RNA polymerization by core Qβ replicase reveal that at the initiation stage, the 3'-adenine of the template RNA provides a stable platform for de novo initiation. EF-Tu in Qβ replicase forms a template exit channel with the β-subunit. At the elongation stages, the C-terminal region of the β-subunit, assisted by EF-Tu, splits the temporarily double-stranded RNA between the template and nascent RNAs before translocation of the single-stranded template RNA into the exit channel. Therefore, EF-Tu in Qβ replicase modulates RNA elongation processes in a distinct manner from its established function in protein synthesis.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicaseA1289Escherichia coli O157:H7Escherichia virus QbetaMutation(s): 0 
Gene Names: tufA
EC: 2.7.7.48
Find proteins for P14647 (Escherichia phage Qbeta)
Explore P14647 
Go to UniProtKB:  P14647
Find proteins for P0A6N3 (Escherichia coli O157:H7)
Explore P0A6N3 
Go to UniProtKB:  P0A6N3
Find proteins for P0A6P3 (Escherichia coli O157:H7)
Explore P0A6P3 
Go to UniProtKB:  P0A6P3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*UP*C)-3')G9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*AP*AP*CP*GP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3')T13N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GH3
      Query on GH3

      Download CCD File 
      A
      3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O13 P3
      QGYIFQKZZSSUCR-OBXARNEKSA-N
       Ligand Interaction
      CA
      Query on CA

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.41 Å
      • R-Value Free: 0.276 
      • R-Value Work: 0.230 
      • R-Value Observed: 0.232 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 139.31α = 90
      b = 256.58β = 90
      c = 101.59γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      MOLREPphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2012-01-18
        Type: Initial release
      • Version 1.1: 2013-09-11
        Changes: Database references
      • Version 1.2: 2017-06-28
        Changes: Source and taxonomy