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 C onserved A ssembly in G ram-negative bacteria and E ukaryotes). 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.