4L8H: Bacteriophage Qbeta coat protein in complex with RNA operator hairpin

Citation:
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 Qbeta bound to its cognate translational operator. The RNA binding mode of Qbeta 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 Qbeta 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 beta strands E and F of Qbeta 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 Qbeta coat protein recognizes and discriminates in favor of its cognate RNA.
PDB ID: 4L8HDownload
MMDB ID: 114095
PDB Deposition Date: 2013/6/17
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Escherichia virus Qbeta
Similar Structures:
Biological Unit for 4L8H: trimeric; determined by author and by software (PISA)
Molecular Components in 4L8H
Label Count Molecule
Proteins (2 molecules)
2
Coat Protein
Molecule annotation
Nucleotide(1 molecule)
1
RNA Operator Hairpin
Molecule annotation
Chemicals (6 molecules)
1
6
* Click molecule labels to explore molecular sequence information.

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