Fig. 4. Conformational changes of the S domain of human 7SL RNA during assembly. (A) The structure of the S domain of human 7SL RNA in complex with M.jannaschii SRP19 (PDB code:1L9A; Oubridge et al., 2002). SRP19 binds to the tetra-loops of helices 6 and 8, clamping them and allowing them to lie side by side. This interaction reduces the flexibility of the asymmetric loop in helix 8 and partially pre-organizes the binding site for SRP54. (B) The binding of the M domain of SRP54 induces a striking conformational change in the structure of the asymmetric loop (PDB code: 1MFQ; Kuglstatter et al., 2002). (C) In the binary complex, the bases of the shorter strand of the asymmetric loop continuously stack, but the longer strand still retains substantial flexibility. (D) In the ternary complex, the asymmetric loop collapses and the G187–C212 base pair (yellow) becomes directly stacked onto the G182–A215 base pair (blue) (Kuglstatter et al., 2002). The bases of A184, C185, C186 and A183 continuously stack, forming a structure reminiscent of the RNA platform seen in the E.coli Ffh–4.5S RNA complex (Batey et al., 2000). A213 and A214 flip out and form A minor motif interactions with the G135–C162 and G136–C161 base pairs of helix 6. This figure was generated using Ribbons (http://sgce.cbse.uab.edu/ribbons/). For an animation of the SRP S domain assembly, see http://www.mssm.edu/students/jovinl02/research/srp_assembly_movie.html