ZAK-alpha is a sensor of mRNA stasis at the ribosomal exit channe

Combining Alphafold3 prediction and RNA crosslinking and immunoprecipitation (CLIP), we uncover that ZAK-alpha dynamically monitors the mRNA exit channel of elongating ribosomes for mRNA stasis. This is accomplished by ZAKa via its direct interactions with the ribosomal proteins RACK1 and RPS27 as well as with the 18S rRNA helix-26.

In this conformation, four mRNA-binding peptides in ZAK-alpha span across the path of ribosome-exiting mRNA. Progressive elongation effectively threads ZAK-alpha off the ribosome, while mRNA stasis stabilizes the interaction allowing for kinase activation. Prolonged binding of ZAK-alpha to slow_x0002_elongating, stalled and collided ribosomes is associated with sequestration of the inhibitory SAM domain on RACK1.