4L8H

Bacteriophage Qbeta coat protein in complex with RNA operator hairpin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2013.08.025

  • 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 inf ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein
A, B
132Escherichia phage QbetaMutation(s): 4 
Find proteins for P03615 (Escherichia phage Qbeta)
Go to UniProtKB:  P03615
Entity ID: 2
MoleculeChainsLengthOrganism
RNA operator hairpinR20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.840α = 90.00
b = 75.840β = 90.00
c = 303.490γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
MAR345data collection
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-17 
  • Released Date: 2013-10-02 
  • Deposition Author(s): Rumnieks, J., Tars, K.

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Data collection, Refinement description