33bf | pdb_000033bf
Single particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment
Structural highlights
FunctionFER_RHORT Cargo protein of a type 1 encapsulin nanocompartment. A ferritin-like ferroxidase that mineralizes iron inside the encapsulin nanocompartment. Converts Fe(2+) to Fe(3+) that is released to the exterior of the decameric complex for deposition in the encapsulin nanocompartment. In solution the decamer binds 10-15 iron cations; in the encapsulin nanocompartment the decamer can bind up to 48 ions, perhaps via its internal channel and on its exterior. The empty encapsulin nanocompartment sequesters about 2200 Fe ions while the cargo-loaded nanocompartment can maximally sequester about 4150 Fe ions. EncFtn retains ferroxidase activity when encapsulated (PubMed:27529188). Flux in the active site di-iron metal center is thought to be controlled by the 'entry site' of the protein, which both attracts metal and controls the rate of iron oxidation (Probable). Encapsulation in the nanocompartment does not alter either function of this protein (PubMed:32878987).[1] [2] [3] Publication Abstract from PubMedEncapsulins are self-assembling protein nanocompartments found in bacteria and archaea that encapsulate cargo enzymes to protect the cell from their toxic reaction products or intermediates. Developments in cryo-electron microscopy (cryo-EM) data processing strategies have enabled encapsulins and their cargo proteins to be investigated together in greater detail. In this study, we present the single particle cryo-EM structure of the Rhodospirillum rubrum encapsulin in both the presence and absence of its partner encapsulated ferritin (EncFtn). Single particle icosahedral reconstructions of empty and loaded encapsulins revealed a higher degree of conformational flexibility at the five-fold pore in the cargo loaded encapsulin. We applied a new non-point group averaging workflow to analyze the encapsulated ferritins within the encapsulin nanocompartment, to produce the first fully refined in situ atomic model of the EncFtn at 2.8 A resolution. Masked 2D classification and particle subtraction demonstrate that cargo loading is heterogeneous in this recombinant complex, with the encapsulin able to house up to five of the decameric EncFtn complexes. Our data provides new insights into the dynamics and cargo arrangement in encapsulins and demonstrates an adaptable workflow for high resolution reconstruction of encapsulin cargoes. Single particle cryo-EM analysis of the Rhodospirillum rubrum encapsulin nanocompartment shows variable loading of encapsulated ferritin cargo proteins and differences in the fivefold pore.,McIver Z, He D, Ross J, Cozzaglio M, Piergentili C, Dornau A, Sumpner N, Brady F, Bialik K, McCorvie T, Sissi C, Basle A, Clarke DJ, Marles-Wright J J Struct Biol. 2026 Sep;218(3):108357. doi: 10.1016/j.jsb.2026.108357. Epub 2026 , Aug 15. PMID:42603627[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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