5NJ8 | pdb_00005nj8

Structural basis for aryl hydrocarbon receptor mediated gene activation

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	ECH_1	e5nj8D1	A: alpha bundles	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (develop294)
B	ECH_1	e5nj8B1	A: alpha bundles	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (develop294)
C	ECH_1	e5nj8C1	A: alpha bundles	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (develop294)
A	ECH_1	e5nj8A1	A: alpha bundles	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (utative)
B	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (utative)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (utative)
A	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00989	PAS fold (PAS)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5 ...	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5].	Domain
B, D	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain		Domain
A, C	PF00989	PAS fold (PAS)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5 ...	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5].	Domain
A, C	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, H	DNA (5'-D(GPGPTPTPGPCPGPTPGPAPCPC)-3')	-	-	-
E, G	DNA (5'-D(GPGPTPCPAPCPGPCPAPAPCPC)-3')	-	-	-
B, D	Aryl hydrocarbon receptor nuclear translocator	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding 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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding 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 protein heterodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific identical protein binding protein homodimerization activity nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity signaling receptor binding aryl hydrocarbon receptor binding	developmental process cellular developmental process cell differentiation cellular process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration regulation of cellular process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process developmental process cellular developmental process cell differentiation cellular process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration regulation of cellular process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of purine nucleotide catabolic process positive regulation of nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process regulation of biological process positive regulation of phosphorus metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process positive regulation of ATP metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process regulation of phosphorus metabolic process regulation of nucleotide catabolic process positive regulation of carbohydrate metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process regulation of metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process catabolic process energy derivation by oxidation of organic compounds positive regulation of nucleotide metabolic process positive regulation of purine nucleotide catabolic process positive regulation of biological process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process positive regulation of cellular process nucleotide catabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process positive regulation of glycolytic process biological regulation ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of catabolic process regulation of glycolytic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of catabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process positive regulation of small molecule metabolic process purine ribonucleoside diphosphate catabolic process regulation of protein sumoylation regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of post-translational protein modification positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process regulation of vascular endothelial growth factor production regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process positive regulation of cytokine production cellular response to stimulus positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction response to stimulus signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of vascular endothelial growth factor receptor signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway regulation of response to stimulus positive regulation of vascular endothelial growth factor receptor signaling pathway regulation of cell communication response to growth factor positive regulation of signaling regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus negative regulation of biological process response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response positive regulation of hormone metabolic process regulation of hormone biosynthetic process regulation of hormone metabolic process regulation of hormone levels hormone metabolic process positive regulation of hormone biosynthetic process regulation of biological quality hormone biosynthetic process placenta development chordate embryonic development animal organ development embryo development in utero embryonic development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching anatomical structure development embryonic organ development response to oxidative stress cellular response to chemical stimulus cellular response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress regulation of developmental process homeostatic process cell development regulation of cell differentiation regulation of cell development positive regulation of developmental process positive regulation of cell differentiation regulation of immune system process myeloid cell homeostasis erythrocyte homeostasis regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic 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 aryl hydrocarbon receptor complex receptor complex nuclear aryl hydrocarbon receptor complex intracellular protein-containing complex nuclear body
A, C	Aryl hydrocarbon receptor	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region 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 cis-regulatory region sequence-specific DNA binding TBP-class protein binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity Hsp90 protein binding heat shock protein binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein heterodimerization activity protein dimerization activity identical protein binding protein homodimerization activity transcription coregulator binding transcription coactivator binding E-box binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process response to stimulus response to chemical response to xenobiotic stimulus regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process apoptotic process cell death programmed cell death regulation of adaptive immune response immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process adaptive immune response response to toxic substance rhythmic process circadian regulation of gene expression circadian rhythm RNA metabolic process regulation of primary 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity regulation of response to biotic stimulus negative regulation of response to biotic stimulus immune response to tumor cell negative regulation of biological process negative regulation of immune response to tumor cell negative regulation of response to tumor cell negative regulation of lymphocyte mediated immunity regulation of response to tumor cell response to biotic stimulus T cell mediated immune response to tumor cell negative regulation of T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of T cell mediated immunity response to tumor cell negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process regulation of immune response to tumor cell negative regulation of adaptive immune response immune effector process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity negative regulation of immune system process negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity developmental process multicellular organism development multicellular organismal process anatomical structure development vasculature development blood vessel development system development circulatory system development positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of RNA biosynthetic process negative regulation of cellular 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 response to stimulus response to 2,3,7,8-tetrachlorodibenzodioxine cellular response to chemical stimulus cellular response to 2,3,7,8-tetrachlorodibenzodioxine regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to cAMP biological process involved in interspecies interaction between organisms response to other organism cellular response to molecule of bacterial origin cellular response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin cellular response to xenobiotic stimulus xenobiotic metabolic process regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation regulation of multicellular organismal process regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation B cell activation cell activation B cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation response to ketone response to lipid response to alcohol cellular response to forskolin cellular response to alcohol response to forskolin cellular response to lipid cellular response to ketone	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle aryl hydrocarbon receptor complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle aryl hydrocarbon receptor complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle receptor complex nuclear aryl hydrocarbon receptor complex intracellular protein-containing complex cytosolic aryl hydrocarbon receptor complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR050933	Circadian Clock Transcription Factors	Family
B, D	IPR013767	PAS fold	Domain
B, D	IPR001067	Nuclear translocator	Family
B, D	IPR000014	PAS domain	Domain
B, D	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B, D	IPR035965	PAS domain superfamily	Homologous Superfamily
B, D	IPR001610	PAC motif	Repeat
B, D	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR013655	PAS fold 3	Domain
A, C	IPR039091	Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor	Family
A, C	IPR035965	PAS domain superfamily	Homologous Superfamily
A, C	IPR001610	PAC motif	Repeat
A, C	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR033348	Aryl hydrocarbon receptor, basic helix-loop-helix domain	Domain
A, C	IPR013767	PAS fold	Domain
A, C	IPR000014	PAS domain	Domain
A, C	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P27540	melanoma Neoplasms, Experimental cirrhosis of liver endometriosis colorectal cancer cutaneous melanoma malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis squamous cell carcinoma heart disease large cell medulloblastoma osteosarcoma skin basal cell carcinoma drug-induced liver injury melanoma Neoplasms, Experimental cirrhosis of liver endometriosis colorectal cancer cutaneous melanoma malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis squamous cell carcinoma heart disease large cell medulloblastoma osteosarcoma skin basal cell carcinoma drug-induced liver injury metabolic syndrome X ovarian cancer atypical teratoid rhabdoid tumor childhood acute lymphoblastic leukemia colorectal carcinoma glioblastoma
A, C	Pharos: P35869	rheumatoid arthritis silicosis congenital nystagmus breast carcinoma Tachycardia ulcerative colitis obesity disorder contact dermatitis pneumonia metabolic disease cancer hypertensive disorder nicotine dependence vascular disease liver cancer rheumatoid arthritis silicosis congenital nystagmus breast carcinoma Tachycardia ulcerative colitis obesity disorder contact dermatitis pneumonia metabolic disease cancer hypertensive disorder nicotine dependence vascular disease liver cancer peanut allergic reaction male infertility bladder calculus breast cancer ureter cancer liver disease prostate cancer atherosclerosis splenic disease malignant pancreatic neoplasm squamous cell carcinoma hereditary diffuse gastric adenocarcinoma melanoma cystic fibrosis pancreatic neoplasm lung adenocarcinoma arteriosclerosis disorder peripheral neuropathy gastric cancer malignant glioma genetic endocrine growth disease bone resorption disease hydrolethalus syndrome ureter benign neoplasm congenital heart disease osteosarcoma pancreatic ductal adenocarcinoma diabetes mellitus liver neoplasm adenoma drug-induced liver injury lung cancer pilocytic astrocytoma pneumonitis exocrine pancreatic carcinoma gastric carcinoma malignant mesothelioma large cell medulloblastoma ovarian cancer cutaneous melanoma acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm androgenetic alopecia peripheral nervous system disease lung carcinoma retinitis pigmentosa gastric neoplasm benign neoplasm

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.