Induced structural changes of 7SL RNA during the assembly of human signal recognition particle

Abstract

The eukaryotic signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein particle that targets secretory and membrane proteins to the endoplasmic reticulum. The binding of SRP54 to the S domain of 7SL RNA is highly dependent on SRP19. Here we present the crystal structure of a human SRP ternary complex consisting of SRP19, the M domain of SRP54 and the S domain of 7SL RNA. Upon binding of the M domain of SRP54 to the 7SL RNA-SRP19 complex, the asymmetric loop of helix 8 in 7SL RNA collapses. The bases of the four nucleotides in the long strand of the asymmetric loop continuously stack and interact with the M domain, whereas the two adenines in the short strand flip out and form two A-minor motifs with helix 6. This stabilizing interaction is only possible when helix 6 has been positioned parallel to helix 8 by the prior binding of SRP19 to the tetraloops of helices 6 and 8. Hence, the crystal structure of the ternary complex suggests why SRP19 is necessary for the stable binding of SRP54 to the S domain RNA.

Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle

“…2A). A similar structural change has been observed in human SRP RNA upon M domain binding (29). The asymmetric loop and helix 6 are in direct contact via A-minor-type interactions formed between the G-C and reversed A-U base pairs flanking the 195-ACC bulge and the looped-out adenosines, A176 and A177.…”

“…of SRP19 to the tips of helices 6 and 8 causes a backbone inversion in the 195-ACC bulge so that its bases become splayed out on the surface of the RNA helix (27). The structure of the ternary complex presented here reveals that, on interaction with SRP54, these bases become stably stacked forming a structure similar to the ''RNA platform'' observed in bacterial and human SRP (28,29). Importantly, the formation of the RNA platform involves an upward movement of the bulged backbone.…”

“…The helix-turnhelix motif in the SRP54 M domain (Gly-324-Leu-427) binds to the widened minor groove of mismatches in the symmetric loop and the invariant A195 in the asymmetric loop of helix 8. The intermolecular contacts between the M. jannaschii M domain and these RNA loops are remarkably conserved to those in the Escherichia coli M domain-SRP RNA (28) and the human M domain-SRP19-SRP RNA (29) complexes. Notably, in the M. jannaschii complex, the M domain and SRP19 are in direct contact by hydrogen-bonding and stacking interactions.…”

“…By comparison, the electron density for the NG domain of B is weaker, and its position is consequently less well defined. It has been shown previously that the asymmetric loop in helix 8 is flexible and undergoes critical structural changes on binding of the SRP54 M domain (20,28,29). In free M. jannaschii 7S.S RNA, the three unpaired bases 195-ACC in the asymmetric loop are pointing toward the interior of the RNA helix (30).…”

Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication

“…The structure of a major part of the M domain with and without RNA has also been determined for E. coli Ffh, human SRP54, and Ffh from Thermus aquaticus (35)(36)(37)(38). The recent structures of the complex of part of the SRP RNA together with SRP19 and the M domain of human SRP54 (38) and of archaeal SRP19 and part of the SRP RNA (39) have provided insights into the assembly of SRP.…”