2IVZ

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF07676	e2ivzA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF07676	ECOD (1.6)
A	PF04052	e2ivzA2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: PF04052	ECOD (1.6)
B	PF07676	e2ivzB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF07676	ECOD (1.6)
B	PF04052	e2ivzB2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: PF04052	ECOD (1.6)
C	PF07676	e2ivzC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF07676	ECOD (1.6)
C	PF04052	e2ivzC2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: PF04052	ECOD (1.6)
D	PF07676	e2ivzD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF07676	ECOD (1.6)
D	PF04052	e2ivzD2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: PF04052	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04052	TolB amino-terminal domain (TolB_N)	TolB amino-terminal domain	TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain.	Domain
A, B, C, D	PF07676	WD40-like Beta Propeller Repeat (PD40)	WD40-like Beta Propeller Repeat	-	Repeat
E, F, G, H	PF03515	Colicin-like bacteriocin tRNase domain (Cloacin)	Colicin-like bacteriocin tRNase domain	-	Family

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	cellular process cell cycle protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process cell cycle protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization amide transport bacteriocin transport cell division membrane organization cellular component organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation membrane invagination regulation of membrane invagination cellular component organization or biogenesis cellular response to stimulus cellular response to nitrogen compound response to bacteriocin response to organic substance response to stimulus response to organonitrogen compound response to endogenous 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 endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound cellular response to bacteriocin response to chemical cellular response to organic substance	membrane cellular anatomical entity 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 endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity 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 response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress 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 response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	intracellular anatomical structure extrachromosomal circular DNA cellular anatomical entity 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 R01GM133198.