Bacteriophage Qbeta coat protein in complex with RNA operator hairpin

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

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This is version 1.3 of the entry. See complete history


Crystal structure of the bacteriophage q beta coat protein in complex with the RNA operator of the replicase gene.

Rumnieks, J.Tars, K.

(2014) J Mol Biol 426: 1039-1049

  • DOI: https://doi.org/10.1016/j.jmb.2013.08.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The coat proteins of single-stranded RNA bacteriophages specifically recognize and bind to a hairpin structure in their genome at the beginning of the replicase gene. The interaction serves to repress the synthesis of the replicase enzyme late in infection and contributes to the specific encapsidation of phage RNA. While this mechanism is conserved throughout the Leviviridae family, the coat protein and operator sequences from different phages show remarkable variation, serving as prime examples for the co-evolution of protein and RNA structure. To better understand the protein-RNA interactions in this virus family, we have determined the three-dimensional structure of the coat protein from bacteriophage Qβ bound to its cognate translational operator. The RNA binding mode of Qβ coat protein shares several features with that of the widely studied phage MS2, but only one nucleotide base in the hairpin loop makes sequence-specific contacts with the protein. Unlike in other RNA phages, the Qβ coat protein does not utilize an adenine-recognition pocket for binding a bulged adenine base in the hairpin stem but instead uses a stacking interaction with a tyrosine side chain to accommodate the base. The extended loop between β strands E and F of Qβ coat protein makes contacts with the lower part of the RNA stem, explaining the greater length dependence of the RNA helix for optimal binding to the protein. Consequently, the complex structure allows the proposal of a mechanism by which the Qβ coat protein recognizes and discriminates in favor of its cognate RNA.

  • Organizational Affiliation

    Biomedical Research and Study Center, Ratsupites 1, Riga LV1067, Latvia.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein
A, B
132Qubevirus durumMutation(s): 4 
Gene Names: coat
Find proteins for P03615 (Escherichia virus Qbeta)
Explore P03615 
Go to UniProtKB:  P03615
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03615
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA operator hairpinC [auth R]20N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.84α = 90
b = 75.84β = 90
c = 303.49γ = 120
Software Package:
Software NamePurpose
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description