6DV3 | pdb_00006dv3

Structure of the Salmonella SPI-1 type III secretion injectisome secretin InvG in the open gate state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	STN domain-like	8057266	3002388	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)
O	Secretin	e6dv3O1	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
O	Secretin_N	e6dv3O3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
O	Secretin_N,PRK15339	e6dv3O2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
N	Secretin	e6dv3N1	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
N	Secretin_N	e6dv3N3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
N	Secretin_N,PRK15339	e6dv3N2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
M	Secretin	e6dv3M3	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
M	Secretin_N	e6dv3M2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
M	Secretin_N,PRK15339	e6dv3M1	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
L	Secretin	e6dv3L2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
L	Secretin_N	e6dv3L3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
L	Secretin_N,PRK15339	e6dv3L1	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
K	Secretin	e6dv3K2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
K	Secretin_N	e6dv3K1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
K	Secretin_N,PRK15339	e6dv3K3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
J	Secretin	e6dv3J1	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
J	Secretin_N	e6dv3J3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
J	Secretin_N,PRK15339	e6dv3J2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
I	Secretin	e6dv3I3	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
I	Secretin_N	e6dv3I1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
I	Secretin_N,PRK15339	e6dv3I2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
H	Secretin	e6dv3H1	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
H	Secretin_N	e6dv3H2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
H	Secretin_N,PRK15339	e6dv3H3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
G	Secretin	e6dv3G2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
G	Secretin_N	e6dv3G1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
G	Secretin_N,PRK15339	e6dv3G3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
F	Secretin	e6dv3F3	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
F	Secretin_N	e6dv3F1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
F	Secretin_N,PRK15339	e6dv3F2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
E	Secretin	e6dv3E2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
E	Secretin_N	e6dv3E1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
E	Secretin_N,PRK15339	e6dv3E3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
D	Secretin	e6dv3D3	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
D	Secretin_N	e6dv3D1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
D	Secretin_N,PRK15339	e6dv3D2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
C	Secretin	e6dv3C2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
C	Secretin_N	e6dv3C1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
C	Secretin_N,PRK15339	e6dv3C3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
B	Secretin	e6dv3B3	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
B	Secretin_N	e6dv3B1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
B	Secretin_N,PRK15339	e6dv3B2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)
A	Secretin	e6dv3A2	A: beta barrels	X: secretin domain (From Topology)	H: secretin domain (From Topology)	T: secretin domain	F: Secretin	ECOD (1.6)
A	Secretin_N	e6dv3A3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
A	Secretin_N,PRK15339	e6dv3A1	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Secretin_N,PRK15339	ECOD (1.6)

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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	PF21304	SPI-1 type 3 secretion system secretin, N0 domain (T3S_SPI-1_N0)	SPI-1 type 3 secretion system secretin, N0 domain	SPI-1 type 3 secretion system secretin forms a ring-shaped multimeric structure which is used to inject bacterial effector proteins into eukaryotic host cells [1-3]. It consists of several N-terminal short domains and a C-terminal secretin domain (P ...	SPI-1 type 3 secretion system secretin forms a ring-shaped multimeric structure which is used to inject bacterial effector proteins into eukaryotic host cells [1-3]. It consists of several N-terminal short domains and a C-terminal secretin domain (Pfam:PF00263). This entry represents the N-terminal N0 domain.	Domain

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	Protein InvG	identical protein binding protein binding binding	establishment of protein localization nitrogen compound transport 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 establishment of protein localization nitrogen compound transport 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 secretion by the type III secretion system transmembrane transport protein transmembrane transport	protein-containing complex type II protein secretion system complex type III protein secretion system complex cell periphery cell outer membrane cellular anatomical structure external encapsulating structure 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	IPR003522	Type III secretion system outer membrane pore YscC/HrcC	Family
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	IPR049034	SPI-1 type 3 secretion system secretin, N0 domain	Domain

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

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 III Secretion Systems	T3S injectisome needle complex: Periplasmic domains of PrgH and PrgK