Nature research paper: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria
, AF2 prediction models 1-5 as predicted through the API from the Söding lab. The SMR domain is predicted with high confidence, while the linker to the N-terminal helix appears flexible., AF2 prediction of the interaction between SmrB and uS2. For this prediction uS2 was fused to the C-terminus of SmrB with a glycine serine linker . The prediction shows the N-terminal helix of SmrB folded back onto uS2., Adjustment of the AF2 predicted model of SmrB-uS2.
However, there was no density for the SMR domain of the second SmrB, indicating a high degree of flexibility due to the lack of another ribosome in front of the stalled one. Bottom: in the control disome without SmrB, there is no density for the N-terminus of SmrB., Comparison of the AF2 prediction, the homology model, and the adjusted model of SmrB. Compared to the AF2 prediction, the homology model is missing the two N-terminal helices and most of the loops are slightly different .
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