8YVD | pdb_00008yvd

Cryo-EM structure of carboxysomal midi-shell: icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 16)

External Resource: Annotation

Domain Annotation: SCOP2 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)
P	SCOP2B Superfamily	EutN/CcmL-like	8036790	3000362	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CcmK-like	8040240	3001326	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
P	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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	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
Q [auth X], R [auth Y]	Carboxysome assembly protein CsoS2B	structural molecule activity structural constituent of carboxysome shell	viral gene expression viral process viral translational frameshifting viral translation metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle
P	Carboxysome shell vertex protein CsoS4A	-	metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	Major carboxysome shell protein CsoS1A	structural molecule activity structural constituent of carboxysome shell	metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
Q [auth X], R [auth Y]	IPR020990	Carboxysome assembly protein CsoS2/2B	Family
P	IPR004992	Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL	Family
P	IPR036677	EutN/Ccml superfamily	Homologous Superfamily
P	IPR014076	Carboxysome shell vertex protein CsoS4A	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR020808	Bacterial microcompartments protein, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR000249	Bacterial microcompartment domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR050575	Bacterial microcompartment shell	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR044872	CcmK/CsoS1, bacterial microcompartment domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	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.