encapsulin nanocompartment

GO:0140737 · Microcompartment · Protein shelled organelle · Proposed

A proteinaceous nanocompartment, 24 to 42 nm across, built from a single HK97-fold shell protein that self-assembles into an icosahedron. Cargo enzymes are packaged inside by a short targeting peptide that binds the shell interior; the commonest cargoes are ferritin-like iron-mineralising proteins and peroxidases. [GO:0140737]

Synonyms: protein nanocompartment

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
encapsulin shell protein	Protein	part of		encA, cfp29	60 subunits (T=1) or 180 (T=3), depending on the family	ESSENTIAL	The single protein that forms the icosahedral shell; it shares the HK97 fold with bacteriophage capsids. `DOI:10.1016/j.cbpa.2016.05.013` Giessen 2016 describes the HK97-fold shell and its T=1 and T=3 assemblies. `DOI:10.1038/nmicrobiol.2017.29` The 2017 survey reports shell families across thousands of genomes.
targeted cargo enzymes	Protein	part of		encB, encC, dyp, flp		DISPENSABLE	Ferritin-like proteins, dye-decolourising peroxidases and others, drawn in by a C-terminal targeting peptide. The shell assembles without them, which is why they are dispensable to the structure. `DOI:10.1016/j.cbpa.2016.05.013` Giessen 2016 describes targeting-peptide-directed cargo loading. `DOI:10.1038/nmicrobiol.2017.29` The 2017 survey classifies encapsulin systems by their cargo.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

encapsulin shell protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:I6WZG6`	Type 1 encapsulin shell protein	enc	Mycobacterium tuberculosis H37Rv (`NCBITaxon:83332`)	REVIEWED
Role and evidence (2 references) The single reviewed UniProtKB entry for gene cfp29, which UniProt lists under the primary name enc, in Mycobacterium tuberculosis H37Rv, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:24855650` Contreras H et al. 2014, ‘Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins.’, J Biol Chem. ECO:0000269 experimental evidence cited by UniProt for the 'Encapsulin nanocompartment' localisation of I6WZG6. `PMID:9596740` Rosenkrands I et al. 1998, ‘Identification and characterization of a 29-kilodalton protein from Mycobacterium tuberculosis culture filtrate recognized by mouse memory effector cells.’, Infect Immun. ECO:0000269 experimental evidence cited by UniProt for the 'Secreted' localisation of I6WZG6.

targeted cargo enzymes

Accession	Protein	Gene	Organism	Entry
`UniProtKB:I6Y4U9`	Dye-decolorizing peroxidase	dyp	Mycobacterium tuberculosis H37Rv (`NCBITaxon:83332`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene dyp in Mycobacterium tuberculosis H37Rv, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:24855650` Contreras H et al. 2014, ‘Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins.’, J Biol Chem. ECO:0000269 experimental evidence cited by UniProt for the 'Encapsulin nanocompartment' localisation of I6Y4U9.

Taxonomic distribution

NCBITaxon:2 Bacteria — VARIABLE: Widely but patchily distributed; the 2017 survey found operons across many phyla. [DOI:10.1038/nmicrobiol.2017.29]
NCBITaxon:2157 Archaea — RARE: Present in a minority of archaeal genomes. [DOI:10.1038/nmicrobiol.2017.29]

Canonical examples

NCBITaxon:1773 Mycobacterium tuberculosis — Source of the first characterised encapsulin, the 'Cfp29' shell with a DyP cargo. [DOI:10.1016/j.cbpa.2016.05.013]

Functions

iron ion sequestration — Ferritin-like cargo mineralises iron inside the shell, buffering the cell against iron and oxidative stress.
- DOI:10.1016/j.cbpa.2016.05.013 Giessen 2016 reviews iron mineralisation as the commonest encapsulin function.
enzyme compartmentalisation — Confines a reaction and its reactive intermediates away from the cytoplasm.
- DOI:10.1038/nmicrobiol.2017.29 The 2017 survey frames encapsulins as a widespread compartmentalisation strategy.

Physical properties

DIAMETER: 24-42 UO:0000018 (T=1 and T=3 shells) [DOI:10.1016/j.cbpa.2016.05.013]

Mechanism graphs

Targeting peptides load iron-mineralising cargo into the shell (FUNCTION)

Encapsulin shell proteins self-assemble into HK97-fold icosahedra, and C-terminal targeting peptides load ferritin-like cargo proteins onto the shell interior. The enclosed cargo oxidises and mineralises iron inside the nanocompartment, storing iron away from the cytosol to buffer iron and oxidative stress.

Subject	Predicate	Object	Evidence
encapsulin shell protein	self-assembles into	encapsulin nanocompartment	`DOI:10.1038/nsmb.1473` Sutter et al. 2008 resolved a Thermotoga maritima encapsulin shell made from 60 shell-protein copies. `DOI:10.1016/j.cbpa.2016.05.013` Giessen 2016 reviews HK97-fold encapsulin shell assembly in T=1 and T=3 architectures.
targeted ferritin-like cargo enzymes	binds	encapsulin shell protein	`DOI:10.1038/nsmb.1473` Sutter et al. 2008 identified conserved binding sites inside the shell for short C-terminal targeting peptides on oxidative-stress enzymes. `DOI:10.1038/s41598-021-84329-z` Altenburg et al. 2021 dissected hydrophobic and ionic interactions that govern targeting-peptide binding to Thermotoga maritima and Myxococcus xanthus encapsulin shells.
encapsulin nanocompartment	encloses	targeted ferritin-like cargo enzymes	`DOI:10.15252/embj.201488566` McHugh et al. 2014 showed that Myxococcus xanthus encapsulin shells are lined with ferritin-like adaptor proteins that nucleate iron-rich granules.
targeted ferritin-like cargo enzymes	mineralises	iron(2+)	`DOI:10.15252/embj.201488566` McHugh et al. 2014 linked ferritin-like encapsulin cargoes with iron sequestration inside the protein shell.
iron(2+)	becomes	ferric mineral core	`DOI:10.15252/embj.201488566` McHugh et al. 2014 observed dense iron-rich cores in native Myxococcus xanthus encapsulins.
ferric mineral core	buffers	iron and oxidative-stress buffering	`DOI:10.15252/embj.201488566` McHugh et al. 2014 tied the Myxococcus xanthus encapsulin system to iron storage and oxidative-stress protection.

HK97-fold shells assemble around peptide-tagged cargo (ASSEMBLY)

Type 1 encapsulin shell protomers form HK97-fold icosahedral cages. Short cargo targeting peptides bind pockets on the shell interior during assembly, producing a closed nanocompartment that selectively encloses enzyme cargo.

Subject	Predicate	Object	Evidence
encapsulin shell protein	folds as	HK97-fold shell protomer	`DOI:10.1038/nsmb.1473` Sutter et al. 2008 resolved the Thermotoga maritima encapsulin shell and found an HK97-like shell-protein fold.
HK97-fold shell protomer	self-assembles into	encapsulin nanocompartment	`DOI:10.15252/embj.201488566` McHugh et al. 2014 resolved the 180-subunit Myxococcus xanthus EncA shell and its ferritin-like cargo. `DOI:10.1016/j.cbpa.2016.05.013` Giessen 2016 reviews T=1 and T=3 encapsulin shell architectures.
targeted cargo enzymes	exposes	C-terminal cargo targeting peptide	`DOI:10.1021/acs.biochem.6b00294` Cassidy-Amstutz et al. 2016 identified minimal peptide tags that load proteins into Thermotoga maritima encapsulins in vivo and in vitro.
C-terminal cargo targeting peptide	binds	shell-interior peptide binding pocket	`DOI:10.1038/s41598-021-84329-z` Altenburg et al. 2021 characterized and engineered targeting-peptide interactions with Thermotoga maritima and Myxococcus xanthus shell interiors.
shell-interior peptide binding pocket	recruits	targeted cargo enzymes	`DOI:10.1038/nsmb.1473` Sutter et al. 2008 identified conserved binding sites for targeting peptides on the inside of the Thermotoga maritima shell.
encapsulin nanocompartment	encloses	targeted cargo enzymes	`DOI:10.15252/embj.201488566` McHugh et al. 2014 showed ferritin-like cargoes enclosed inside native Myxococcus xanthus encapsulin shells.

Evidence

DOI:10.1016/j.cbpa.2016.05.013 Giessen TW 2016, 'Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science', Current Opinion in Chemical Biology.
DOI:10.1038/nmicrobiol.2017.29 'Widespread distribution of encapsulin nanocompartments reveals functional diversity', Nature Microbiology 2017.

Curation history

2026-09-02T04:49:54Z claude · CREATED_RECORD — Drafted from the cited reviews; every GO term, taxon id and DOI resolved live before writing. Not yet human-reviewed.
2026-09-04T01:17:11Z codex · ADD_CAUSAL_GRAPH — Added a FUNCTION graph for targeting-peptide cargo loading and ferritin-like iron mineralisation inside encapsulin shells, with primary evidence from Sutter et al. 2008 and McHugh et al. 2014.
2026-09-04T04:22:00Z codex · ADD_CAUSAL_GRAPH — Added an ASSEMBLY graph for HK97-fold shell self-assembly around targeting-peptide-tagged cargo, grounded ferrous iron with ChEBI, and anchored shell protein nodes with Pfam.
2026-09-08T07:39:50Z uniprot_genes · SEED_PROTEIN_EXAMPLES — #183: added 2 protein example(s) by resolving each of the component's declared gene symbols to the single reviewed UniProtKB entry for that symbol in a taxon this record names, deduplicated by accession. Symbols resolving to more than one reviewed entry were skipped rather than chosen between.

Source: data/structures/microcompartment/encapsulin_nanocompartment.yaml