2IVZ | pdb_00002ivz

Structure of TolB in complex with a peptide of the colicin E9 T- domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2ivzd1	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	TolB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2ivzd2	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	TolB, N-terminal domain	TolB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2ivzc1	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	TolB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2ivzc2	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	TolB, N-terminal domain	TolB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2ivzb1	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	TolB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2ivzb2	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	TolB, N-terminal domain	TolB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2ivza1	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	TolB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2ivza2	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	TolB, N-terminal domain	TolB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	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)
D	FG-GAP, FG-GAP_3	e2ivzD1	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: FG-GAP, FG-GAP_3	ECOD (v294.1)
D	Pribosyltran	e2ivzD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
C	FG-GAP, FG-GAP_3	e2ivzC1	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: FG-GAP, FG-GAP_3	ECOD (v294.1)
C	Pribosyltran	e2ivzC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
B	FG-GAP, FG-GAP_3	e2ivzB1	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: FG-GAP, FG-GAP_3	ECOD (v294.1)
B	Pribosyltran	e2ivzB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
A	FG-GAP, FG-GAP_3	e2ivzA1	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: FG-GAP, FG-GAP_3	ECOD (v294.1)
A	Pribosyltran	e2ivzA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
D	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
C	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
C	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
B	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
B	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
A	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
A	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07676	WD40-like Beta Propeller Repeat (PD40)	WD40-like Beta Propeller Repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PROTEIN TOLB	protein binding binding protein domain specific binding protein-containing complex binding	cell septum assembly cytokinesis cellular component biogenesis cellular component organization cellular component assembly cytokinetic process cellular process cell cycle cell division cellular component organization or biogenesis cell cycle process protein import localization establishment of protein localization cell septum assembly cytokinesis cellular component biogenesis cellular component organization cellular component assembly cytokinetic process cellular process cell cycle cell division cellular component organization or biogenesis cell cycle process protein import localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization nitrogen compound transport bacteriocin transport membrane organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation membrane invagination regulation of membrane invagination cellular response to nitrogen compound cellular response to stimulus response to bacteriocin response to stimulus response to oxygen-containing compound response to nitrogen compound response to antibiotic cellular response to oxygen-containing compound cellular response to antibiotic cellular response to chemical stimulus cellular response to bacteriocin response to chemical	cellular anatomical structure membrane cell division site periplasmic space outer membrane-bounded periplasmic space cell envelope protein-containing complex
E, F, G, H	COLICIN-E9	protein binding binding protein domain specific binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus	intracellular anatomical structure cellular anatomical structure extrachromosomal circular DNA extrachromosomal DNA protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A, B, C, D	IPR007195	TolB, N-terminal	Domain
A, B, C, D	IPR011659	WD40-like beta-propeller	Repeat
A, B, C, D	IPR014167	Tol-Pal system protein TolB	Family
E, F, G, H	IPR024575	Cloacin/colicin	Family
E, F, G, H	IPR016128	Pyosin/cloacin translocation domain	Domain
E, F, G, H	IPR044925	His-Me finger superfamily	Homologous Superfamily
E, F, G, H	IPR024566	Colicin, receptor domain	Domain
E, F, G, H	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
E, F, G, H	IPR037146	Colicin/pyocin, DNase domain superfamily	Homologous Superfamily

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.