Extended Data Fig. 4: Orientation of the P-site monomer in the PTC is affected minimally by the presence or absence of a N-terminal formyl group.

a, Superposition and b, close-up view of the PTC regions of 1VY4 (purple and teal) with that of 8EMM, the cryo-EM model reported here (rose and green). 23S rRNA is shown in white. Two structures are shown for 1VY4 because there are two ribosome structures in the unit cell. c, Superposition of the PTC regions of 1VY4 with the lowest energy pose of the metadynamics simulation of the RRM (in which the P-site tRNA has been altered in silico to carry fMet). The identity of the models 8EMM, 1VY4, and the RRM are indicated for both A and P sites with model−matched colors. These images reveal excellent superposition of the carbonyl groups (red) that are attacked during amide bond formation and the three P-site N atoms (in blue), regardless of whether that N is attached to protons alone or a formyl group. This analysis suggests that the presence or absence of a formyl group on the P-site tRNA has little or no effect on monomer placement within the PTC from the standpoint of structural biology.