5WQ9 | pdb_00005wq9

CryoEM structure of type II secretion system secretin GspD G453A mutant in Vibrio cholerae

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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)
A	CagX	e5wq9A1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
A	C1-set	e5wq9A4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
C	CagX	e5wq9C1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
C	C1-set	e5wq9C5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
D	CagX	e5wq9D1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
D	C1-set	e5wq9D5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
E	CagX	e5wq9E1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
E	C1-set	e5wq9E5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
G	CagX	e5wq9G2	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
G	C1-set	e5wq9G5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
H	CagX	e5wq9H1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
H	C1-set	e5wq9H4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
I	CagX	e5wq9I1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
I	C1-set	e5wq9I5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
J	CagX	e5wq9J2	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
J	C1-set	e5wq9J5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
K	CagX	e5wq9K1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
K	C1-set	e5wq9K5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
L	CagX	e5wq9L1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
L	C1-set	e5wq9L4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
M	CagX	e5wq9M1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
M	C1-set	e5wq9M4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
N	CagX	e5wq9N1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
N	C1-set	e5wq9N4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
O	CagX	e5wq9O1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
O	C1-set	e5wq9O5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
F	CagX	e5wq9F1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
F	C1-set	e5wq9F4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)
B	CagX	e5wq9B2	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: CagX	ECOD (v294.1)
B	C1-set	e5wq9B5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: C1-set	ECOD (v294.1)

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: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Type II Secretion Systems	GspD secretin

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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