The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes

We describe the identification and three-dimensional (3D) structure determination of an approx. 1 MDa, hollow, elliptical protein cage discovered while surveying proteins isolated from the ciliary matrix of the ciliate Tetrahymena thermophila. By using mass spectrometry, AlphaFold, and cryo-electron microscopy, we identified the cage-like protein and determined its stoichiometry, mid-resolution 3D structure, and protein interactions. A sequence survey revealed several thousand homologs, with conservation across eukaryotic microbes spanning green algae, fungi, amoebozoans, choanoflagellates, and SAR organisms, as well as deep homology to genes in gram-negative predominantly marine prokaryotes and microbial mats, implying an ancient origin and arguing against a eukaryote-specific function. We subsequently isolated and solved the structure to high resolution from the slime mold Dictyostelium discoideum. Based on these observations, we named this assembly the CAGE complex (for Conserved Assembly in Gram-negative bacteria and Eukaryotes). We speculate on potential roles as a chaperone, container, or protease trap, but the biological function of the CAGE complex has yet to be determined.