6H3N | pdb_00006h3n

Structure of VgrG1 in the Type VI secretion VgrG1-Tse6-EF-Tu complex embedded in lipid nanodiscs

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)
C	Anoctamin	e6h3nC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.1)
B	Anoctamin	e6h3nB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.1)
A	Anoctamin	e6h3nA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF22178	Bacteriophage T4 gp5 C-terminal trimerisation domain (Gp5_trimer_C)	Bacteriophage T4 gp5 C-terminal trimerisation domain	-	Repeat
A, B, C	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	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	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	IPR017847	Type VI secretion system, RhsGE-associated Vgr family subset	Family
A, B, C	IPR050708	Type VI secretion system VgrG/RHS	Family
A, B, C	IPR006531	Gp5/Type VI secretion system Vgr protein, OB-fold domain	Domain
A, B, C	IPR037026	Vgr protein, OB-fold domain superfamily	Homologous Superfamily
A, B, C	IPR054030	Gp5/Type VI secretion system Vgr, C-terminal trimerisation domain	Domain
A, B, C	IPR006533	Type VI secretion system, RhsGE-associated Vgr protein	Family

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.