Characterization of Iron Oxide Nanoparticles Inside the Myxococcus xanthus Encapsulin

Encapsulins are microbial protein nanocompartments that spatially organize and sequester specific biochemical processes, including iron storage. While their protein shells have been extensively characterized, the composition and structure of their mineral cores remain less understood. Here, we use bright field transmission electron microscopy (BF TEM), high-angle annular dark-field scanning TEM (HAADF STEM), energy-dispersive X-ray (EDX), and electron energy-loss spectroscopy (EELS) in STEM to characterize the iron-containing mineral granules within the Myxococcus xanthus encapsulin system at near atomic resolution. We find that the internal nanoparticles are smaller (~2 nm) and more numerous (up to ~2200 per encapsulin) than previously reported. These nanoparticles are typically amorphous and have a composition consistent with FePO₄ (measured Fe:P ratio of ≈1:1.2). Each encapsulin contains on average ~8500 iron atoms, corresponding to a volumetric density of 2.1 atoms/nm³. Phosphorus incorporation inhibits crystallization, whereas growth in phosphorus-free media leads to the formation of nano-crystalline goethite [α-FeO(OH)].