2Y9K | pdb_00002y9k

Three-dimensional model of Salmonella's needle complex at subnanometer resolution

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)
B	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	STN domain-like	8057266	3002388	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)
D	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
F	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)
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	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	STN domain-like	8057266	3002388	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	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Secretin repeat domain-like	8057265	3002387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	STN domain-like	8057266	3002388	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)
E	SCOP2B Superfamily	STN domain-like	8057266	3002388	SCOP2B (2022-06-29)
E	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)
B	Ribosomal_S6e	e2y9kB2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
B	PI3K_rbd,PIK3CG_ABD	e2y9kB3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
C	Ribosomal_S6e	e2y9kC2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
C	PI3K_rbd,PIK3CG_ABD	e2y9kC3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
D	Ribosomal_S6e	e2y9kD2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
D	PI3K_rbd,PIK3CG_ABD	e2y9kD3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
F	Ribosomal_S6e	e2y9kF2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
F	PI3K_rbd,PIK3CG_ABD	e2y9kF3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
L	Ribosomal_S6e	e2y9kL2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
L	PI3K_rbd,PIK3CG_ABD	e2y9kL3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
O	Ribosomal_S6e	e2y9kO2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
O	PI3K_rbd,PIK3CG_ABD	e2y9kO3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
N	Ribosomal_S6e	e2y9kN2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
N	PI3K_rbd,PIK3CG_ABD	e2y9kN3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
M	Ribosomal_S6e	e2y9kM2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
M	PI3K_rbd,PIK3CG_ABD	e2y9kM3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
K	Ribosomal_S6e	e2y9kK2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
K	PI3K_rbd,PIK3CG_ABD	e2y9kK3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
J	Ribosomal_S6e	e2y9kJ2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
J	PI3K_rbd,PIK3CG_ABD	e2y9kJ3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
I	Ribosomal_S6e	e2y9kI2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
I	PI3K_rbd,PIK3CG_ABD	e2y9kI3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
H	Ribosomal_S6e	e2y9kH2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
H	PI3K_rbd,PIK3CG_ABD	e2y9kH3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
G	Ribosomal_S6e	e2y9kG2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
G	PI3K_rbd,PIK3CG_ABD	e2y9kG3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
E	Ribosomal_S6e	e2y9kE2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
E	PI3K_rbd,PIK3CG_ABD	e2y9kE3	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)
A	PI3K_rbd,PIK3CG_ABD	e2y9kA1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (develop294)

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	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 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 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