3MMP

Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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This is version 1.2 of the entry. See complete history


Literature

Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins.

Kidmose, R.T.Vasiliev, N.N.Chetverin, A.B.Andersen, G.R.Knudsen, C.R.

(2010) Proc Natl Acad Sci U S A 107: 10884-10889

  • DOI: 10.1073/pnas.1003015107
  • Primary Citation of Related Structures:  
    3MMP

  • PubMed Abstract: 
  • The RNA-dependent RNA polymerase core complex formed upon infection of Escherichia coli by the bacteriophage Qbeta is composed of the viral catalytic beta-subunit as well as the host translation elongation factors EF-Tu and EF-Ts, which are required for initiation of RNA replication ...

    The RNA-dependent RNA polymerase core complex formed upon infection of Escherichia coli by the bacteriophage Qbeta is composed of the viral catalytic beta-subunit as well as the host translation elongation factors EF-Tu and EF-Ts, which are required for initiation of RNA replication. We have determined the crystal structure of the complex between the beta-subunit and the two host proteins to 2.5-A resolution. Whereas the basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, a unique C-terminal region of the beta-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome. The evolution of resistance by the host appears to be impaired because of the interactions of the beta-subunit with parts of EF-Tu essential in recognition of aminoacyl-tRNA.


    Organizational Affiliation

    Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Tu 2, Elongation factor TsA, C678Escherichia coli K-12Mutation(s): 0 
Gene Names: tufBb3980JW3943tsfb0170JW0165
UniProt
Find proteins for P0A6P1 (Escherichia coli (strain K12))
Explore P0A6P1 
Go to UniProtKB:  P0A6P1
Find proteins for P0CE48 (Escherichia coli (strain K12))
Explore P0CE48 
Go to UniProtKB:  P0CE48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0A6P1P0CE48
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase beta chainD [auth F],
B [auth G]
589Escherichia virus QbetaMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P14647 (Escherichia virus Qbeta)
Explore P14647 
Go to UniProtKB:  P14647
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14647
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PXN
Query on PXN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol
C17 H36 O8
GXEZGLLPFFKHGE-FPCVCCKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.71α = 90
b = 139.4β = 92.06
c = 101.87γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy