Structural studies of ribosomal RNA based on cross-analysis of comparative models and three-dimensional crystal structures

Basepair mapping of the rRNAs in the high-resolution crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits not only proved the authenticity of covariation analysis in predicting RNA secondary structures with high accuracy, but also provided a great wealth of information on RNA structure, ranging from diverse basepair conformations to structure motifs. Based on cross-analysis of comparative structure models and crystal structures of rRNAs, a systematic and unambiguous classification for basepair conformations is established, and the structural features and biological implications for a wide variety of RNA sequence and structure motifs, including the AA.AG@helix.ends motif, the sticky motif consisting of AGUA/GAA, GUA/GAA, and GGA/GAA motifs, and the lonepair triloop motif, are discussed.