4R71

Structure of the Qbeta holoenzyme complex in the P1211 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for RNA-genome recognition during bacteriophage Q beta replication.

Gytz, H.Mohr, D.Seweryn, P.Yoshimura, Y.Kutlubaeva, Z.Dolman, F.Chelchessa, B.Chetverin, A.B.Mulder, F.A.Brodersen, D.E.Knudsen, C.R.

(2015) Nucleic Acids Res. 43: 10893-10906

  • DOI: 10.1093/nar/gkv1212

  • PubMed Abstract: 
  • Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying ...

    Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spectroscopy, as well as sequence conservation, surface electrostatic potential and mutational analyses to decipher the roles of the β-subunit and the first two oligonucleotide-oligosaccharide-binding domains of S1 (OB1-2) in the recognition of Qβ (+)-RNA by the Qβ replicase complex. We show how three basic residues of the β subunit form a patch located adjacent to the OB2 domain, and use NMR spectroscopy to demonstrate for the first time that OB2 is able to interact with RNA. Neutralization of the basic residues by mutagenesis results in a loss of both the phage infectivity in vivo and the ability of Qβ replicase to amplify the genomic RNA in vitro. In contrast, replication of smaller replicable RNAs is not affected. Taken together, our data suggest that the β-subunit and protein S1 cooperatively bind the (+)-stranded Qβ genome during replication initiation and provide a foundation for understanding template discrimination during replication initiation.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Ts, Elongation factor Tu
A, C
694Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufB, tsf
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Find proteins for P0A6P1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6P1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase beta chain
B, D
595Escherichia phage QbetaMutation(s): 0 
EC: 2.7.7.48
Find proteins for P14647 (Escherichia phage Qbeta)
Go to UniProtKB:  P14647
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S1
E, F
171Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsA (ssyF)
Find proteins for P0AG67 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG67
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.730α = 90.00
b = 115.450β = 96.14
c = 178.520γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PXIIIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references