2D5V

Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
E [auth A]	d2d5va2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth A]	d2d5va1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	CUT domain	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth B]	d2d5vb2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth B]	d2d5vb1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	CUT domain	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth A]	PF00046	e2d5vA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
E [auth A]	PF02376	e2d5vA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF02376	ECOD (1.6)
F [auth B]	PF00046	e2d5vB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
F [auth B]	PF02376	e2d5vB2	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF02376	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E [auth A]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
F [auth B]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
F [auth B]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF02376	CUT domain (CUT)	CUT domain	The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein (eg Swiss:P10180).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], C [auth E]	5'-D(TPCPTPAPAPGPTPCPAPAPTPAPAPT)-3'	-	-	-
B [auth D], D [auth F]	5'-D(APTPTPAPTPTPGPAPCPTPTPAPGPA)-3'	-	-	-
E [auth A], F [auth B]	Hepatocyte nuclear factor 6	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein-containing complex binding chromatin binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein-containing complex binding chromatin binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cell adhesion regulation of biological process regulation of cellular process cell-matrix adhesion regulation of cell-matrix adhesion developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cell adhesion regulation of biological process regulation of cellular process cell-matrix adhesion regulation of cell-matrix adhesion regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion cellular process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process leukocyte differentiation epithelium development endocrine system development tissue development epithelial cell differentiation glandular epithelial cell differentiation pancreas development endocrine pancreas development pancreatic A cell differentiation enteroendocrine cell differentiation columnar/cuboidal epithelial cell differentiation endoderm development anatomical structure morphogenesis cell migration cell motility organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization cell projection assembly monosaccharide metabolic process carbohydrate metabolic process organic substance metabolic process hexose metabolic process small molecule metabolic process metabolic process primary metabolic process glucose metabolic process immune system development spleen development hematopoietic or lymphoid organ development pancreatic D cell differentiation cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cell fate commitment positive regulation of locomotion regulation of cell motility positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion positive regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process type B pancreatic cell differentiation Notch signaling pathway positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process epithelial cell development	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR001356	Homeobox domain	Domain
E [auth A], F [auth B]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR003350	CUT domain	Domain
E [auth A], F [auth B]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

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.