Extended Data Fig. 2: Sequence and structural diversity in archaeal PTCs.
From: Structure of an archaeal ribosome reveals a divergent active site and hibernation factor
a, Shannon entropy plot for PTC nucleotides in GTDB bacteria and archaea. Positions indicated by a * have a Shannon entropy value of zero for archaea. A Shannon entropy value of zero corresponds to complete conservation of the nucleotide, while a value of 1.386 corresponds to an equal distribution of all four nucleotides. b, Distribution of rare PTC sequences in Nanoarchaeota archaea. The cladogram is derived from the GTDB phylogeny, where branches with bootstrap support <50% are colored in grey. The letter o represents order and n represents the number of 23S rRNA sequences in each distribution. Nucleotides that differ from the archaeal consensus sequence are shown in color. c-e, Cryo-EM density for regions of the PTC shown in Fig. 2. Water molecules and magnesium ions are shown as red and green spheres respectively. f, Secondary structures of the H. marismortui and P. calidifontis A loops. Positions with rare sequence variation, 2554 and 2555, are highlighted in red in the P. calidifontis A loop. g, Comparison of the apical region of the A loop in H. marismortui PDB:1S72 ref. 45 (blue) and P. calidifontis (purple). h, Cryo-EM density for the P. calidifontis A loop. Base stacking interactions are shown as dashed lines.
