4IQR | pdb_00004iqr

Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038367	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068350	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038367	3001442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068350	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038367	3001442	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068350	3000068	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068350	3000068	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038367	3001442	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	ACR_tran	e4iqrA5	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: ACR_tran	ECOD (v294.1)
B	DCD	e4iqrB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: DCD	ECOD (v294.1)
F	DNA_pol_B_exo1	e4iqrF1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: DNA_pol_B_exo1	ECOD (v294.1)
E	DNA_pol_B_exo1	e4iqrE1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: DNA_pol_B_exo1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
B	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
F	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
F	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
E	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
E	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF00105	Double treble clef zinc finger, C4 type (zf-C4)	Double treble clef zinc finger, C4 type	In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.	Domain
A, B, E, F	PF00104	Ligand-binding domain of nuclear hormone receptor (Hormone_recep)	Ligand-binding domain of nuclear hormone receptor	This all helical domain is involved in binding the hormone in these receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L	Nuclear receptor coactivator 2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding sequence-specific DNA 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 protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding sequence-specific DNA 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development positive regulation of biological process tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process response to ketone response to lipid response to stimulus response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to hormone stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular receptor signaling pathway intracellular signal transduction peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear body
D, H	DNA (5'-D(CPCPTPGPAPCPCPTPTPTPGPAPCPCPTPAPGPTPTPC)-3')	-	-	-
C, G	DNA (5'-D(GPGPAPAPCPTPAPGPGPTPCPAPAPAPGPGPTPCPAPG)-3')	-	-	-
A, B, E, F	Hepatocyte nuclear factor 4-alpha	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity signaling receptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity protein binding signaling receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding fatty acid binding organic acid binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding chromatin binding identical protein binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding metal ion binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding phospholipid homeostasis chemical homeostasis homeostatic process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding phospholipid homeostasis chemical homeostasis homeostatic process lipid homeostasis triglyceride homeostasis acylglycerol homeostasis regulation of biological process regulation of growth regulation of cellular component organization regulation of cellular process negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular process cellular component organization or biogenesis developmental process regulation of embryonic development regulation of multicellular organismal development regulation of gastrulation regulation of developmental process embryonic morphogenesis embryo development gastrulation multicellular organism development anatomical structure morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of localization establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling hormone secretion protein localization to extracellular region cell communication localization peptide secretion regulation of secretion by cell secretion by cell signal release intracellular protein localization regulation of peptide hormone secretion regulation of signaling regulation of transport secretion regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell cell-cell signaling regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion cellular response to stimulus cellular response to nitrogen compound response to peptide hormone regulation of signal transduction cellular response to growth hormone stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus regulation of growth hormone receptor signaling pathway response to hormone signal transduction enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus growth hormone receptor signaling pathway cell surface receptor signaling pathway response to endogenous stimulus cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to growth hormone cellular response to chemical stimulus regulation of response to stimulus response to chemical regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression signal transduction involved in regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription glucose homeostasis carbohydrate homeostasis negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular developmental process cell differentiation regulation of lipid metabolic process lipid metabolic process rhythmic process circadian rhythm regulation of circadian rhythm ornithine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process regulation of small molecule metabolic process regulation of ornithine metabolic process regulation of amino acid metabolic process small molecule metabolic process sterol homeostasis cholesterol homeostasis response to hexose response to monosaccharide response to carbohydrate response to glucose cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation reproductive process sex differentiation developmental process involved in reproduction	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
I, J, K, L	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
I, J, K, L	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
I, J, K, L	IPR017426	Nuclear receptor coactivator	Family
I, J, K, L	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
I, J, K, L	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
I, J, K, L	IPR013767	PAS fold	Domain
I, J, K, L	IPR000014	PAS domain	Domain
I, J, K, L	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
I, J, K, L	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
I, J, K, L	IPR035965	PAS domain superfamily	Homologous Superfamily
I, J, K, L	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
I, J, K, L	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
I, J, K, L	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, B, E, F	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B, E, F	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B, E, F	IPR050274	Nuclear hormone receptor family NR2 subfamily	Family
A, B, E, F	IPR001723	Nuclear hormone receptor	Family
A, B, E, F	IPR049635	Hepatocyte nuclear factor 4, ligand-binding domain	Domain
A, B, E, F	IPR049636	Hepatocyte nuclear factor 4-like, DNA-binding domain	Domain
A, B, E, F	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B, E, F	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I, J, K, L	Pharos: Q15596	breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm testicular germ cell tumor breast cancer endogenous depression glioblastoma medulloblastoma plasma cell myeloma
A, B, E, F	Pharos: P41235	maturity-onset diabetes of the young ulcerative colitis Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young type 2 diabetes mellitus maturity-onset diabetes of the young type 1 renal cysts and diabetes syndrome hyperinsulinism due to HNF4A deficiency hyperinsulinemic hypoglycemia metabolic syndrome X acquired metabolic disease Diabetes Mellitus, Non-Insulin-Dependent hyperinsulinism large cell medulloblastoma pancreatic ductal adenocarcinoma cancer maturity-onset diabetes of the young ulcerative colitis Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young type 2 diabetes mellitus maturity-onset diabetes of the young type 1 renal cysts and diabetes syndrome hyperinsulinism due to HNF4A deficiency hyperinsulinemic hypoglycemia metabolic syndrome X acquired metabolic disease Diabetes Mellitus, Non-Insulin-Dependent hyperinsulinism large cell medulloblastoma pancreatic ductal adenocarcinoma cancer gallbladder disease intellectual disability liver disease pancreatic intraductal papillary-mucinous neoplasm diabetes mellitus inborn errors of metabolism intestinal disease malignant glioma