Fig. 3.

3D structure of the 5S rRNA. (A) The large subunit of Haloarcula marismotui (PDB: 1NJI) [49] is docked in the density (left, view from the 30S side; right, view from the solvent side of the 50S subunit); only the 5S rRNA is shown colored, and the insert is marked by *. Coloring is by nucleotide: adenines, green; cytosines, orange; guanines, red; and uracils, blue. Cp—central protuberance; St—stalk. The scale bar indicates 50 Å. (B) The section of the map corresponding to the 5S rRNA is cropped out for visualization. The Haloarcula marismortui 5S rRNA was mutated to match the sequence of the Halococcus morrhuae 5S, except that the insert (whose secondary structure is not known) was omitted, and rigidly docked inside the density. The insertion site is marked by *. The scale bar indicates 5 Å. (C) The section of the map corresponding to the 5S rRNA is cropped out of the published, 6.6 Å Methanothermobacter thermautotrophicus cryo‐EM map and associated atomic model (EMD‐2012, PDB 4ADX) [37] and colored as in (B). This and all other homolog maps lack the protruding lump of density seen in (B). Scale is identical to panel B.