1PP7 | pdb_00001pp7

Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin Inr

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)
C [auth U]	d1pp7u_	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)
C [auth U]	SCOP2 Family	IBP3 DNA-binding domain-like	8003144	4000219	SCOP2 (2022-06-29)
C [auth U]	SCOP2 Superfamily	Winged helix DNA-binding domain	8003145	3000034	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth U]	IBD	e1pp7U1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: IBD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth U]	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
C [auth U]	39 kDa initiator binding protein	cation binding ion binding binding metal ion binding small molecule binding	-	-
B [auth F]	FERREDOXIN INR	-	-	-
A [auth E]	FERREDOXIN INR	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth U]	IPR018845	Initiator binding domain	Domain
C [auth U]	IPR036184	IBP39, C-terminal domain superfamily	Homologous Superfamily
C [auth U]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth U]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth U]	IPR024238	Initiator binding protein 39kDa, C-terminal	Domain

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.