1PP8

crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element

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)
I [auth U]	d1pp8u_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
J [auth P]	d1pp8p_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
K [auth F]	d1pp8f_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
L [auth V]	d1pp8v_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
M	d1pp8m_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
N [auth O]	d1pp8o_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	39 kda initiator binding protein, IBP39, N-terminal domain	39 kda initiator binding protein, IBP39, N-terminal domain	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth U]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2B (2022-06-29)
J [auth P]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2B (2022-06-29)
L [auth V]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2B (2022-06-29)
N [auth O]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003145	3000034	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)
I [auth U]	PF10416	e1pp8U1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)
J [auth P]	PF10416	e1pp8P1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)
K [auth F]	PF10416	e1pp8F1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)
L [auth V]	PF10416	e1pp8V1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)
M	PF10416	e1pp8M1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)
N [auth O]	PF10416	e1pp8O1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF10416	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth U]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
J [auth P]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
K [auth F]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
L [auth V]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
M	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
N [auth O]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	PF10416	Transcription-initiator DNA-binding domain IBD (IBD)	Transcription-initiator DNA-binding domain IBD	In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognised by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr bindin ...	In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognised by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr binding domain, IBD, connected via a flexible, proteolytically sensitive, linker (residues 127-145) to a C-terminal domain. The IBD structure reveals a winged-helix-wing conformation with each element binding to DNA, the central helix-turn-helix contributing the majority of the specificity-determining contacts with the Inr core motif TCAPy(T/A). The binding of IBP39 to the Inr directly recruits RNA polymerase II and in this way initiates transcription [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth I], C [auth Y], D [auth K]	ALPHA-SCS INR	-	-	-
E [auth T], F [auth R], G [auth J], H [auth G]	ALPHA-SCS INR	-	-	-
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	39 kDa initiator binding protein	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	IPR018845	Initiator binding domain	Domain
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	IPR036184	IBP39, C-terminal domain superfamily	Homologous Superfamily
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
I [auth U], J [auth P], K [auth F], L [auth V], M, I [auth U], J [auth P], K [auth F], L [auth V], M, N [auth O]	IPR024238	Initiator binding protein 39kDa, C-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.