SRP9/14 binding to PhAlu SRP RNA. (A) Overall structure of the chimeric Alu domain RNP. The backbone of PhAlu134 RNA is drawn as a ribbon and colored purple and cyan for the 5′ and 3′ domains, respectively. The hSRP9 and hSRP14 are drawn as, respectively, red and green cartoons. SRP14 contacts exclusively the 5′ and 3′ domain whereas SRP9 contacts both RNA domains. The long internal loop, which extends toward the J1/2/5 junction, is shown dotted where poorly visible. The basic C-terminal extension of SRP14 extends toward the S-domain. (B) Comparison of PhAlu134 RNA with the human Alu RNA structure model. A structural superposition of the human Alu domain model, derived from the structure of a circularly permutated RNA (Weichenrieder et al. 2000) (yellow backbone with bases as sticks) onto PhAlu134 RNA (red) highlights the highly conserved tertiary fold of the Alu RNA core from divergent organisms. Superposing just the 5′ domain (nucleotides 15–65 in PhAlu and 2–47 in human Alu RNA) allows matching of 31 nt (19 identities) with an RMSD of 1.47 Å. For the 5′ and 3′ domain taken together, 53 bases can be matched (26 identities) with an RMSD of 1.77 Å. (C) Diagram showing how both the 5′ domain and 3′ stem of PhAlu134 RNA are accommodated side by side within the concave β-sheet surface of SRP9/14. (D) Protein–RNA interactions mediated by SRP9 at the t3 tertiary interaction. SRP9 (red with yellow side chains) interacts with nucleotides from both the PhAlu 5′ (purple) and 3′ (cyan) domains thus reinforcing the t3 tertiary RNA interaction.
