To store iron and regulate its metabolism, cells have developed ferritin-based organelles: classical ferritins and bacterioferritins that function in iron storage and Dps proteins that normally function in iron detoxification . Bacteria additionally possess other kinds of protein-based organelles, which allow them to encapsulate enzymes and/or to sequester toxic or volatile products . Myxococcus xanthus produces such protein-based particles that accumulate iron in its encapsulin nanocompartment, which is composed of the HK97-like shell protein EncA and three minor proteins, EncB, EncC and EncD . These particles have dense iron-rich cores. We used cryo-electron microscopy and single particle reconstruction techniques to determine the structure of native encapsulin particles from M. xanthus and recombinant EncA shells produced in E. coli. The 3-D reconstruction of native particles shows them to have the same T=3 icosahedral shell as recombinant particles but filled with dense trilaminar material, which electron tomography shows to be composed of 11-19 dense granules, ~5.5 nm in diameter and not icosahedrally ordered. Based on STEM mass measurements, we estimated that the granules accommodate ~35,000 Fe atoms, as compared to a maximum of ~4,500 iron atoms in ferritin. In addition to T=3 capsids, recombinant EncA produces smaller particles, mainly T=1 icosahedra. These observations lead to a model for iron-sequestering encapsulin nanocompartments in which EncA encapsulates the minor proteins and EncB and EncC act as mineralizing centers for iron granule assembly.