Ribosomes are macromolecular machines for protein synthesis, and the architectures of cytoplasmic (cyto-) and mitochondrial (mito-) ribosomes reflect many years of coevolution between rRNA and ribosomal proteins to maintain coordinated translation across compartments. Daphnia serves as an exceptional model organism, combining extensive population genetic data with the distinction of possessing the longest reported crustacean cyto-ribosomal rRNA. Also, crustacean ribosomes remain largely unexplored at the molecular level. Here, I will present structural analysis of D. pulex cyto-ribosome using single-particle cryogenic electron microscopy (cryo-EM) method. Our consensus cryo-EM density map allows atomic modeling of both ribosomal subunits with associated tRNA, mRNA, and nascent peptides captured during translation. The structure revealed that the Daphnia ribosome exhibits conserved core features shared with eukaryotic counterparts yet also contains lineage-specific expansions in rRNA and ribosomal proteins. Comparative structural analyses of ribosomes within Daphnia populations and between Daphnia, Drosophila, and human show the structural divergence for functional adaptation. Furthermore, by encoding cryo-EM structural variability into latent space representations, multiple ribosomal states were extracted, revealing a conformational landscape underlying translation regulation. Finally, preliminary cryo-EM structural analysis of Daphnia mito-ribosomes will be presented, outlining a structural framework for investigating cyto-mito ribosomal coevolution and its role in coordinating protein synthesis across cellular compartments.
