Figure 2.

Substrate location in the pocket suggested to represent the remnant of the proto-ribosome and the proposed reaction transition state. In all panels, the A- and P-sub-regions of the symmetrical region as well as the A-site and P-site tRNAs are shown in blue and green, respectively, and the ribosome components are shown in grey. The red rod indicates the position of the imaginary symmetry axis and the red dot indicates a section cut parallel to its direction. (a) A cartoon representing the translocation of the A-site tRNA into the P-site. The main motion of the tRNA helical region is represented by the horizontal arrow and rotatory motion of the A-site tRNA 3′ end is represented by the curved arrow. The so-derived position of the 3′ end of the P-site tRNA is also shown (in green). The ribosome scaffold that guides the motion is represented by the grey ‘ribs’. (b) The volume consumed by the motion is shown as a net, obtained by snapshots of the rotatory motion of the A-site 3′ end (every 15° around the imaginary rotation axis (not shown here)). The transition state analogue that is formed during the rotary motion, just before reaching the P-site [18] is shown in orange. (c) The RNA backbone of the pocket suggested to represent the remnant of the proto-ribosome with the tRNAs 3′ ends, highlighting the connections between the two halves (by the red stars). The A-site substrate (blue) was obtained by cutting out (computationally) the acceptor stem from the crystal structure of complexes of the tRNA acceptor stem and the 3′ end mimic with D50S [10]. The P-site substrate was derived from the A-site amino acid by applying the rotatory motion. The box shows a GNRA tetra loop that contains the A-minor motif (the bases involved are shown in magenta and yellow). (d) The symmetrical region superposed on the interface surface of the large ribosomal subunits, with its inner core of 120 nucleotides shown in full line, and the shell containing the A- and P-loops shown in broken lines.