Encapsulin-Ferritin Model

Tom Goddard
March 21, 2022

Encapsulin-ferritin iron storage nano-machine.
Encapsulin proteins (blue), ferritin proteins (brown, red) and linkers (yellow), iron crystals (red, white, blue).

Here are notes on how I made a rough encapsulin-ferritin model in ChimeraX 1.3, session file encapsulin.cxs. This bacterial nanomachine stores iron, converting the soluble iron +2 oxidation state to a non-soluble +3 oxidation state that forms nano-crystals. Sixty copies of the encapsulin protein forms a virus-like icosahedral shell and inside are forty copies of a ferritin protein that catalyses the iron storage.

Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment.
Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, Zarazua-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, Basle A, Clarke DJ, Marles-Wright J.
Sci Adv. 2022 Jan 28;8(4):eabj4461. doi: 10.1126/sciadv.abj4461.

Proteins and Electron Microscopy

I fit 12 pentamers of encapsulin (PDB 7oe2) and 4 decamers of ferritin (PDB 5n5f) into an asymmetric single particle reconstruction EMDB 12873 (3.5 Å), by hand placing them with the move model mouse mode and using the ChimeraX fitmap command.

Peptide Linkers

The ferritin proteins have a 40 amino acid C-terminal tail containing a 9 amino acid signal sequence (GSLGIGSLR) that binds in a groove on the encapsulin protein. These are not seen in electron microscopy. To get a sense of the space occupied by these linkers I took a model of the disordered linker from an AlphaFold prediction for UniProt D0LZ73 residues 92-131. I made 40 copies of this linker, aligning one end to each of the ferritin proteins and pulling the other end to an encapsulin groove using molecular dynamics using some custom Python code in ChimeraX.

Iron oxide crystals

To get a picture of what the hydrated iron oxide crystals formed inside the encapsulin shell might look like I made 2 nanometer crystals of a ferrihydrite model using the ChimeraX unitcell tool to make 4 by 4 by 2 unit cells together with some custom Python to get the bonds right.

The structure of ferrihydrite, a nanocrystalline material.
Michel FM, Ehm L, Antao SM, Lee PL, Chupas PJ, Liu G, Strongin DR, Schoonen MA, Phillips BL, Parise JB.
Science. 2007 Jun 22;316(5832):1726-9. doi: 10.1126/science.1142525.

Virtual Reality

A simpler model made in virtual reality was made in an NIH Virtual and Augmented Reality Scientific Interest Group webinar.