Fig. 4.
Changes in the position of the head domain in the 30S subunit in state R2. (A) Bridge B1 in ribosomes in state R1 (14). The tRNAs bound in the 30S subunit A site (yellow), and in the P/P (orange) and E/E sites (red) are shown. Domains in protein S13 in the 30S subunit head domain (blue) and protein L5 in the 50S subunit (purple) are marked. An asterisk marks the approximate location of the A-site finger (ASF) helix H38 in 23S rRNA, the tip of which is disordered in the crystal structure (14). Protein L31, not seen in E. coli 70S ribosome structures, has been removed for clarity. (B) Bridge B1 in the apo-70S ribosome in state R2 (light blue) compared to state RF (red). Domains in protein S13 in the 30S subunit head domain and protein L5 in the 50S subunit are marked. Asterisk as in panel A. (C) Position of full-length tRNAs modeled onto the apo-70S ribosome in state R2. The superposition used the head domain of the 30S subunit in the fully-rotated state RF (16) for reference (1, 11). Surfaces of the modeled tRNAs (yellow and orange) are compared to the position of tRNAs in state R1 (14), as described in panel A and shown as ribbons. (D) Position of full-length tRNA in the P site of state R1 (14) modeled onto the ribosome complexed with ASLMetf in the P site in state R2 (11), using the 30S subunit body and platform of the ribosome in state R1 as a reference. Surface of the modeled tRNA (blue) is compared to the position of the P-site ASLMetf in state R2 (blue) and tRNAs in state R1 (described above) shown as ribbons. (E) Step-wise rearrangements in the ribosome along the ratcheting pathway. The molecular envelope of the 30S subunit is shown for clarity. Domains of the 30S subunit (head, body, platform), tRNA binding sites (A, P, and E, respectively), and bridges B1b, B2a, and B3 are shown. The view is the same as in Fig. 2B. Arrows indicate the direction of movement from one state to the next.