Research Article

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

Figure 5

Various snapshots from multiple simulations of A/T-tRNA and native tRNA are shown, where the time sampled over is >200 ns (Supplementary Movie S1). (a) A/T-site tRNA (shown in purple) moves toward the A-site tRNA (red) which is shown in reverse view of the ribosome density, to illustrate the >70 Å motion covered by the 3′-CCA acceptor end. The tRNA shows an oscillation about the A-site tRNA structure (red) (Divergent stereo). (b) Side view of Figure 5(a) (Divergent stereo). (c) Contact map for tRNA trajectory superposed with the ribosome. (d) The side view panel on right shows the accommodation corridor for the A/T-tRNA in the ribosome. The A/T-tRNA has to make a snug fit because of the narrow space. (e) The lower right panel is zoomed in closer to illustrate the interaction areas.
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