ZAK activation at the collided ribosome

Ribosome collisions activate the ribotoxic stress response (RSR) mediated by the MAP3K ZAKα (ZAK), which in turn regulates downstream phosphorylation of the MAPKs JNK and p38 and cell fate consequences. Despite this critical role during cellular stress, a structural and mechanistic understanding of the ZAK-ribosome interaction and activation have remained elusive. Here, we combine biochemistry with cryo-electron microscopy (cryo-EM) to dissect ZAK interactions with ribosomes in various states both in vivo and in vitro. We identified regions of ZAK necessary for binding to ribosomes under normal and under stress-induced conditions. Moreover, we discovered how interactions between ZAK and the ribosomal protein RACK1 mediate ZAK activation by recognizing the collision-interface. Further, we provide insight into how this process can be negatively regulated to prevent constitutive ZAK activation. Characterizing novel variants as well as a known pathogenic variant of ZAK’s SAM domain supports a key role of this conserved domain in regulating kinase activity on and off the ribosome. Collectively, we show that ZAK directly binds at the collided ribosome interface giving molecular insight into kinase activity regulation at the ribosome. CLIP-seq of ZAK-KO HEK293T cells transfected with different ZAK constructs (Full-length (WT), Activation Loop mutant (ActLoopD), 1-649 truncation (RBRdel), overexpressed Activation Loop Mutant (OX-ActLoopD), or mock (ZAK-KO), treated with or without Anisomycin. Two replicates for each group.