Figure 2

Distribution in the ribosome of modified nucleosides in Halobacteriaceae rRNA. (A) A schematic of secondary structure of H. volcanii 16S rRNA with the locations of the various modified nucleosides indicated with darkened circles. The helices in which these appear are numbered according to the designations used for E. coli (B) The locations of modified nucleosides of H. volcanii 16S rRNA are highlighted in a crystal structure of the small ribosomal subunit derived for Thermus thermophilus (PDB entry 2j00; portion of 70S) by showing full atomic volume (van der Waals radii) darkened on a backbone of the rRNA. The decoding center region is indicated by shading where the anti-codon stem loops of the A, P, and E-site tRNAs sit. (C) A schematic of secondary structure of H. marismortui 23S rRNA with the locations of the various modified nucleosides indicated with darkened circles. (D) The locations of modified nucleosides of H. marismortui 23S rRNA are highlighted in a crystal structure of the large ribosomal subunit derived for Thermus thermophilus as described above. The peptidyl transferase active site is indicated by shading where the acceptor stems of the A- and P-site tRNAs sit. The location of the Ψ residue of H. salinarum is highlighted with an open circle in (C) and lighter gray atomic volume in (D). In (B) and (D), the subunit interface is towards the front.