Protein recognition of a ribosomal RNA tertiary structure

Ribosomal protein L11 recognizes a highly conserved, 58 nucleotide domain of large subunit ribosomal RNA. This domain has a set of tertiary interactions that are specifically stabilized by Mg2+ and NH4+ ions. The protein recognizes this tertiary structure, in the sense that ions stabilizing the tertiary structure also promote L11 binding, and a heat stable form of the protein (from Bacillus stearothermophilus) prevents RNA unfolding. We also find that these RNA-binding properties are confined to a approximately 75 amino acid domain of the protein. The larger issue of L11 function within the ribosome is discussed in light of these findings.