Fig. 3. Secondary structure of SRP RNAs. (A) Escherichia coli, (B) M.jannaschii and (C) H.sapiens. The E.coli 4.5S RNA is 114 nucleotide long and forms an extended hairpin structure. The S domain of M.jannaschii and human 7SL RNA has two branches referred to as helices 6 and 8. Helix 8 bears similarities to domain IV of 4.5S RNA, the binding site for Ffh. The symmetric loop (orange) has the same four non-Watson–Crick base pairs, and the asymmetric loop (red) contains the ACC tri-nucleotide. The dotted lines for M.jannaschii RNA show the interaction between adenines in helix 6 with the backbone in helix 8 found in the SRP19–RNA complex (Hainzl et al., 2002). The dotted lines for human RNA show the A minor motif interactions found in the ternary complex (Kuglstatter et al., 2002).