Abstract
The L1 stalk of the large ribosomal subunit undergoes large-scale movements coupled to the translocation of deacylated tRNA during protein synthesis. We use quantitative comparative structural analysis to localize the origins of L1 stalk movement and to understand its dynamic interactions with tRNA and other structural elements of the ribosome. Besides its stacking interactions with the tRNA elbow, stalk movement is directly linked to intersubunit rotation, rotation of the 30S head domain and contact of the acceptor arm of deacylated tRNA with helix 68 of 23S rRNA. Movement originates from pivoting at stacked non-canonical base pairs in a Family A three-way junction and bending in an internal G-U-rich zone. Use of these same motifs as hinge points to enable such dynamic events as rotation of the 30S subunit head domain and in flexing of the anticodon arm of tRNA suggests that they represent general strategies for movement of functional RNAs.
Highlights
The L1 stalk of the large ribosomal subunit undergoes large-scale movements coupled to the translocation of deacylated tRNA during protein synthesis
What is the functional role of L1 stalk movement? Second, how are its movements coordinated with the numerous other dynamic events associated with ribosomal translocation? Third, what is the structural basis of L1 stalk movement—that is, where exactly does movement originate, and which structural features are responsible? And are there common structural principles underlying the molecular movements observed for different functional RNAs?
We carried out a quantitative comparative structural analysis on a data set of 32 X-ray and cryo-EM structures of ribosome complexes from the Protein DataBank (PDB)[33] in which the L1 stalk was well ordered, which includes both bacterial and eukaryotic ribosome complexes (Supplementary Table 1)
Summary
The L1 stalk of the large ribosomal subunit undergoes large-scale movements coupled to the translocation of deacylated tRNA during protein synthesis. Most extensively studied are the rotational movements of the 30S subunit[5,7,8,9] and its head domain[10,11,12], which play major roles in the movement of the acceptor ends of the tRNAs into their hybrid states, and translocation of the mRNA and anticodon ends of the tRNA, respectively We examine another prominent dynamic feature of the ribosome, the L1 stalk, which undergoes the largest-scale structural movements that have so far been observed for the ribosome, comparable to the largest excursions made by motor proteins[13], during its participation in the translocation process[14,15,16,17,18,19,20,21]. What is the functional role (or roles) of L1 stalk movement? Second, how are its movements coordinated with the numerous other dynamic events associated with ribosomal translocation? Third, what is the structural basis of L1 stalk movement—that is, where exactly does movement originate, and which structural features are responsible? And are there common structural principles underlying the molecular movements observed for different functional RNAs?
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