Molecular Architecture of Encapsulin Nanocompartments:
an Iron-Sequestering Shell that Protect Cells from Oxidative Stress

Juan Fontanaa, Daniel Nemeceka,b, Colleen A. McHughc, Dennis C. Winklera, Naiqian Chenga, J. Bernard Heymanna, Joseph S. Walld, Egbert Hoiczykc, and Alasdair C. Stevenaa

a NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.

b Central European Institute of Technology, Masaryk University, Brno, CZ.

c Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD 21205, USA.

d Department of Biology, Brookhaven National Laboratory, Upton, NY 10973, USA


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 [1]. Bacteria additionally possess other kinds of protein-based organelles, which allow them to encapsulate enzymes and/or to sequester toxic or volatile products [2]. 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 [3]. 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.


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2.         Kerfeld, C.A. et al. (2010) Annu. Rev. Microbiol. 64: 391-408.

3.         McHugh C.A. et al. (2014) EMBO J. 33: 1896-1911.