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bioRxiv · 10.1101/470047

The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

Fu, Z.·Indrisiunaite, G.·Kaledhonkar, S.·Shah, B.·Sun, M.·Chen, B.·Grassucci, R. A.·Ehrenberg, M.·Frank, J.
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Abstract

When the mRNA translating ribosome encounters a stop codon in its aminoacyl site (A site), it recruits a class-1 release factor (RF) to induce hydrolysis of the ester bond between peptide chain and peptidyl-site (P-site) tRNA. This process, called termination of translation, is under strong selection pressure for high speed and accuracy. Class-1 RFs (RF1, RF2 in bacteria, eRF1 in eukarya and aRF1 in archaea), have structural motifs that recognize stop codons in the decoding center (DC) and a universal GGQ motif for induction of ester bond hydrolysis in the peptidyl transfer center (PTC) 70 [A] away from the DC. The finding that free RF2 is compact with only 20 [A] between its codon reading and GGQ motifs came therefore as a surprise1. Cryo-electron microscopy (cryo-EM) then showed that ribosome-bound RF1 and RF2 have extended structures2,3, suggesting that bacterial RFs are compact when entering the ribosome and switch to the extended form in a stop signal-dependent manner3. FRET4, cryo-EM5,6 and X-ray crystallography7, along with a rapid kinetics study suggesting a pre-termination conformational change on the millisecond time-scale of ribosome-bound RF1 and RF28, have lent indirect support to this proposal. However, direct experimental evidence for such a short-lived compact conformation on the native pathway to RF-dependent termination is missing due to its transient nature. Here we use time-resolved cryo-EM9,10,11,12,13 to visualize compact and extended forms of RF1 and RF2 at 3.5 and 4 [A] resolution, respectively, in the codon-recognizing complex on the pathway to termination. About 25% of ribosomal complexes have RFs in the compact state at 24 ms reaction time after mixing RF and ribosomes, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.

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Fu, Z., Indrisiunaite, G., Kaledhonkar, S., Shah, B., Sun, M., Chen, B., Grassucci, R. A., Ehrenberg, M., Frank, J.. 2018-11-14. The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. https://doi.org/10.1101/470047

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