Fig. 4: PepNL blocks RF2-mediated translation termination.
From: A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism
a Overview of the RF2 structure within the PepNL-arrested ribosome (cyan) compared with the active RF2 (purple, PDB: 6C5L). The P-tRNAAsp (green) and pepNL mRNA (brown) are also shown. b Close-up view of the apical loop conformations of the rearranged and active RF2 states. Gln252s of the GGQ motif are highlighted as sticks with sphere models. The ribosome is shown as a surface model. Hydrogen bond interactions between the apical loop of the rearranged RF2 and 23S rRNA. c: Arg245 and G2508, Gln252 and G2583, Val254 and C2573, Arg256 and U2554, Gly251 and G2553. d: Glu258-Gln280 and U2492, His281 and U2460. e: Arg262 and G2557. f Superimposition of the active RF2 (purple) indicates a steric clash of its Gln252 with Ile13 of PepNL. The distorted Ile13 of the PepNL peptide occupies the pocket formed by A2451, C2452, and U2506 (not shown) of 23S rRNA, blocking the proper accommodation of the RF2 apical loop. The rRNA nucleotides and Ile13 are shown as sphere models. g Schematics representing the mechanism of RF2 inhibition by the PepNL nascent peptide.
