Annotations: 5WQ8

CryoEM structure of type II secretion system secretin GspD in Vibrio cholerae

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
O	CagX	e5wq8O2	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
O	C1-set	e5wq8O5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
N	CagX	e5wq8N1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
N	C1-set	e5wq8N5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
M	CagX	e5wq8M2	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
M	C1-set	e5wq8M5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
L	CagX	e5wq8L1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
L	C1-set	e5wq8L5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
K	CagX	e5wq8K1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
K	C1-set	e5wq8K5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
J	CagX	e5wq8J1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
J	C1-set	e5wq8J5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
I	CagX	e5wq8I1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
I	C1-set	e5wq8I4	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
H	CagX	e5wq8H1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
H	C1-set	e5wq8H4	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
G	CagX	e5wq8G1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
G	C1-set	e5wq8G5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
F	CagX	e5wq8F1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
F	C1-set	e5wq8F5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
E	CagX	e5wq8E1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
E	C1-set	e5wq8E4	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
D	CagX	e5wq8D1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
D	C1-set	e5wq8D4	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
C	CagX	e5wq8C2	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
C	C1-set	e5wq8C5	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
B	CagX	e5wq8B1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CagX	ECOD (v295.2)
B	C1-set	e5wq8B4	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)
A	C1-set	e5wq8A1	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
O	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
N	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
M	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
L	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
K	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
J	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
I	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
H	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
G	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
F	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
E	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
D	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
A	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	PF03958	Bacterial type II/III secretion system short domain (Secretin_N)	Bacterial type II/III secretion system short domain	This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	PF00263	Bacterial type II and III secretion system protein (Secretin)	Bacterial type II and III secretion system protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	Type II secretion system protein D	identical protein binding protein binding binding	establishment of protein localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport macromolecule localization cellular process intracellular protein localization establishment of protein localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport macromolecule localization cellular process intracellular protein localization protein transport across the cell outer membrane protein secretion by the type II secretion system transmembrane transport protein transmembrane transport	protein-containing complex type II protein secretion system complex cell outer membrane cellular anatomical structure external encapsulating structure extracellular region membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR050810	Bacterial Secretion System Channel Protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR005644	NolW-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR004846	Type II/III secretion system, secretin-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR038591	NolW-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR049371	GspD-like, N0 domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR004845	Type II secretion system protein GspD, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR013356	Type II secretion system protein GspD	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	IPR001775	GspD/PilQ family	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	OPM	Transmembrane	Beta-barrel transmembrane	Outer bacterial membrane secretin	Outer bacterial membrane secretion