6MZX | pdb_00006mzx

Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth A1]	SCOP2B Superfamily	EutN/CcmL-like	8083101	3000362	SCOP2B (2022-06-29)
B [auth A2]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)
C [auth A3]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)
D [auth A4]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)
E [auth A5]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)
F [auth A6]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)
G [auth A7]	SCOP2B Superfamily	CcmK-like	8081332	3001326	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth A1]	EutN_CcmL	e6mzxA11	A: beta barrels	X: OB-fold	H: EutN/CcmL-like (From Topology)	T: EutN/CcmL-like	F: EutN_CcmL	ECOD (1.6)
B [auth A2]	BMC	e6mzxA21	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
C [auth A3]	BMC	e6mzxA31	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
D [auth A4]	BMC	e6mzxA41	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
E [auth A5]	BMC	e6mzxA51	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
F [auth A6]	BMC	e6mzxA61	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
G [auth A7]	BMC	e6mzxA71	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC	ECOD (1.6)
H [auth A8]	BMC_1	e6mzxA82	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC_1	ECOD (1.6)
I [auth A9]	BMC_1	e6mzxA92	A: a+b two layers	X: Alpha-beta plaits	H: CcmK-like (From Topology)	T: CcmK-like	F: BMC_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth A1]	PF03319	Ethanolamine utilisation protein EutN/carboxysome (EutN_CcmL)	Ethanolamine utilisation protein EutN/carboxysome	The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a ...	The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face [2]. EutN is involved in the cobalamin-dependent degradation of ethanolamine [1].	Domain
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	PF00936	BMC domain (BMC)	BMC domain	Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric struc ...	Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure [1].	Domain
H [auth A8], I [auth A9]	PF00936	BMC domain (BMC)	BMC domain	Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric struc ...	Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth A1]	Ethanolamine utilization protein EutN/carboxysome structural protein Ccml	-	-	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	Microcompartments protein HO-5815	-	-	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle
H [auth A8], I [auth A9]	Microcompartments protein HO-5816	-	-	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth A1]	IPR004992	Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL	Family
A [auth A1]	IPR036677	EutN/Ccml superfamily	Homologous Superfamily
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	IPR020808	Bacterial microcompartments protein, conserved site	Conserved Site
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	IPR000249	Bacterial microcompartment domain	Domain
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	IPR050575	Bacterial microcompartment shell	Family
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	IPR044872	CcmK/CsoS1, bacterial microcompartment domain	Domain
B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7]	IPR037233	CcmK-like superfamily	Homologous Superfamily
H [auth A8], I [auth A9]	IPR000249	Bacterial microcompartment domain	Domain
H [auth A8], I [auth A9]	IPR044870	Bacterial microcompartment (BMC) circularly permuted domain	Domain
H [auth A8], I [auth A9]	IPR037233	CcmK-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.