4MTK | pdb_00004mtk

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F		e4mtkF1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
E		e4mtkE1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
D		e4mtkD1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
C	Gp5_trimer_C	e4mtkC6	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Gp5_trimer_C	ECOD (v294.1)
C		e4mtkC2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
B	Gp5_trimer_C	e4mtkB6	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Gp5_trimer_C	ECOD (v294.1)
B		e4mtkB2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
A	Phage_GPD	e4mtkA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Phage_GPD	ECOD (v294.1)
A	Phage_GPD	e4mtkA4	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Phage_GPD	ECOD (v294.1)
A	Phage_base_V, DUF6484	e4mtkA5	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Phage_base_V, DUF6484	ECOD (v294.1)
A	Gp5_trimer_C	e4mtkA6	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Gp5_trimer_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
F	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
F	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
F	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	CATH (4.3.0)
E	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
E	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
E	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
E	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	CATH (4.3.0)
D	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
D	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
D	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
D	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	CATH (4.3.0)
C	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
C	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
C	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
C	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	CATH (4.3.0)
B	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
B	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
B	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	CATH (4.3.0)
A	2.30.110.50	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
A	3.55.50.10	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold	Baseplate protein-like domains	CATH (4.3.0)
A	4.10.220.110	Few Secondary Structures	Irregular	Light-harvesting Protein		CATH (4.3.0)
A	2.40.50.230	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Gp5 N-terminal domain	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	PF04717	Type VI secretion system/phage-baseplate injector OB domain (Phage_base_V)	Type VI secretion system/phage-baseplate injector OB domain	Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft [1]. This entry represents the OB fold part of the structure. This structure contains an unu ...	Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft [1]. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix [3].	Domain
A, B, C, D, E A, B, C, D, E, F	PF22178	Bacteriophage T4 gp5 C-terminal trimerisation domain (Gp5_trimer_C)	Bacteriophage T4 gp5 C-terminal trimerisation domain	-	Repeat
A, B, C, D, E A, B, C, D, E, F	PF05954	Phage tail baseplate hub (GPD) (Phage_GPD)	Phage tail baseplate hub (GPD)	-	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	VgrG1	-	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 transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type VI secretion system macromolecule 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 transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type VI secretion system macromolecule localization cellular process intracellular protein localization	cellular anatomical structure extracellular region type VI protein secretion system complex protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR017847	Type VI secretion system, RhsGE-associated Vgr family subset	Family
A, B, C, D, E A, B, C, D, E, F	IPR050708	Type VI secretion system VgrG/RHS	Family
A, B, C, D, E A, B, C, D, E, F	IPR006531	Gp5/Type VI secretion system Vgr protein, OB-fold domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR037026	Vgr protein, OB-fold domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR054030	Gp5/Type VI secretion system Vgr, C-terminal trimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006533	Type VI secretion system, RhsGE-associated Vgr protein	Family

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Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

4MTK | pdb_00004mtk