Archaea SRP RNA features. (a) Secondary structure of Archaeoglobus fulgidus SRP RNA. (b) Consensus-matching 5e motifs sorted by their taxonomic membership. (c) Mismatching 5e motifs. Helices are numbered from 1 to 8 and helical sections are labeled with letters a to f [33]. For example, helix 1 is composed of residues one to seven which are base paired with residues 303 to 310; helix 2 consists of residues at positions ten to 13 base paired with the residues at positions 59 to 62. The extended helix 5 contains six helical sections, 5a to 5f. Helix 7 is lacking in the SRP RNAs of the archaea. The - and -ends are shown, and residues are labeled in ten-residue increments. Base pairs were determined by comparative sequence analysis [32] and by considering high-resolution data (Table 1). The approximate extents of the large (S) and the small (Alu) domains are indicated. Shown in dark gray are the UGUNR motif (labeled UGU) in the small domain, the 5e motif within helical section 5e at the indicated hinge [34], the GNAR apical tetraloop of helix 6 and the SRP54 binding motif of helix 8 in the large domain. Dashed lines suggest tertiary interactions.
