4UHV

The structure of VgrG1, the needle tip of the bacterial 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)
A	Phage_GPD_1st	e4uhvA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_GPD_1st	ECOD (1.6)
A	Phage_GPD_4th	e4uhvA6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_GPD_4th	ECOD (1.6)
A	Phage_base_V	e4uhvA5	A: beta barrels	X: OB-fold	H: Tail-associated lysozyme gp5-N (From Topology)	T: Tail-associated lysozyme gp5-N	F: Phage_base_V	ECOD (1.6)
A	VI_Rhs_Vgr	e4uhvA4	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: VI_Rhs_Vgr	ECOD (1.6)
A	Phage_GPD_2nd	e4uhvA2	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: Phage_GPD_2nd	ECOD (1.6)
A	Phage_GPD_3rd	e4uhvA3	A: a+b complex topology	X: C-terminal insertion domain in phage tail proteins (From Topology)	H: C-terminal insertion domain in phage tail proteins (From Topology)	T: C-terminal insertion domain in phage tail proteins	F: Phage_GPD_3rd	ECOD (1.6)
B	Phage_GPD_1st	e4uhvB5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_GPD_1st	ECOD (1.6)
B	Phage_GPD_4th	e4uhvB6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_GPD_4th	ECOD (1.6)
B	Phage_base_V	e4uhvB3	A: beta barrels	X: OB-fold	H: Tail-associated lysozyme gp5-N (From Topology)	T: Tail-associated lysozyme gp5-N	F: Phage_base_V	ECOD (1.6)
B	VI_Rhs_Vgr	e4uhvB4	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: VI_Rhs_Vgr	ECOD (1.6)
B	Phage_GPD_2nd	e4uhvB1	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: Phage_GPD_2nd	ECOD (1.6)
B	Phage_GPD_3rd	e4uhvB2	A: a+b complex topology	X: C-terminal insertion domain in phage tail proteins (From Topology)	H: C-terminal insertion domain in phage tail proteins (From Topology)	T: C-terminal insertion domain in phage tail proteins	F: Phage_GPD_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	PF22178	Bacteriophage T4 gp5 C-terminal trimerisation domain (Gp5_trimer_C)	Bacteriophage T4 gp5 C-terminal trimerisation domain	-	Repeat
A, B	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	VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1	-	protein localization establishment of protein localization cellular 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 transmembrane transport localization secretion by cell protein transmembrane transport protein localization establishment of protein localization cellular 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 transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type VI secretion system cellular macromolecule localization macromolecule localization cellular process	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	IPR017847	Type VI secretion system, RhsGE-associated Vgr family subset	Family
A, B	IPR050708	Type VI secretion system VgrG/RHS	Family
A, B	IPR006531	Gp5/Type VI secretion system Vgr protein, OB-fold domain	Domain
A, B	IPR037026	Vgr protein, OB-fold domain superfamily	Homologous Superfamily
A, B	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.