4CN7 | pdb_00004cn7

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to an idealized DR1 Response Element

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	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	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	zf-C4	e4cn7A1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
B	zf-C4	e4cn7B1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
E	zf-C4	e4cn7E1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
F	zf-C4	e4cn7F1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)

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)
B	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	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)
F	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E, F	RETINOIC ACID RECEPTOR RXR-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 transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor 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 transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity LBD domain binding protein domain specific binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity retinoic acid binding organic acid binding isoprenoid binding retinoid binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding identical protein binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear vitamin D receptor binding retinoic acid-responsive element 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 nuclear steroid receptor activity DNA binding domain binding peptide binding cation binding transition metal ion binding zinc ion binding metal ion binding enzyme binding	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux multicellular organismal process regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process multicellular organism development positive regulation of biomineral tissue development ossification anatomical structure development biomineral tissue development regulation of multicellular organismal process developmental process regulation of multicellular organismal development bone mineralization animal organ development tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification cellular response to stimulus regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular process signal transduction nuclear receptor-mediated signaling pathway cellular response to hormone stimulus nervous system development system development peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression mRNA transcription mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process negative regulation of biological process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 regulation of macromolecule metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process 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 nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular developmental process cell differentiation response to retinoic acid response to lipid response to oxygen-containing compound positive regulation of cell communication regulation of response to nutrient levels positive regulation of signal transduction regulation of signal transduction cellular response to vitamin D response to vitamin D positive regulation of intracellular signal transduction cellular response to oxygen-containing compound cellular response to nutrient levels regulation of response to stimulus cellular response to lipid regulation of vitamin D receptor signaling pathway response to nutrient levels response to vitamin positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling response to nutrient vitamin D receptor signaling pathway cellular response to vitamin positive regulation of vitamin D receptor signaling pathway regulation of cell communication cellular response to nutrient positive regulation of signaling regulation of thyroid hormone receptor signaling pathway positive regulation of thyroid hormone receptor signaling pathway thyroid hormone receptor signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome receptor complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome receptor complex membrane-bounded organelle mitochondrion intracellular membrane-bounded organelle RNA polymerase II transcription regulator complex nucleus nuclear protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	5'-D(CPTPAPGPGPTPCPAPAPAPGPGPTPCP APGP)-3'	-	-	-
D, H	5'-D(CPTPGPAPCPCPTPTPTPGPAPCPCPTP APGP)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B, E, F	IPR021780	Nuclear/hormone receptor activator site AF-1	Domain
A, B, E, F	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B, E, F	IPR000003	Retinoid X receptor/HNF4	Family
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	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
A, B, E, F	Pharos: P19793	prostate cancer lesion of sciatic nerve sciatic neuropathy thyroid gland carcinoma amyotrophic lateral sclerosis type 1 thyroid adenoma malignant mesothelioma Sciatic Neuritis thyroid cancer astrocytic tumor invasive ductal breast carcinoma MALT lymphoma osteosarcoma pituitary cancer B-cell chronic lymphocytic leukemia prostate cancer lesion of sciatic nerve sciatic neuropathy thyroid gland carcinoma amyotrophic lateral sclerosis type 1 thyroid adenoma malignant mesothelioma Sciatic Neuritis thyroid cancer astrocytic tumor invasive ductal breast carcinoma MALT lymphoma osteosarcoma pituitary cancer B-cell chronic lymphocytic leukemia lung carcinoma medulloblastoma ovarian cancer primary cutaneous T-cell lymphoma interstitial cystitis large cell medulloblastoma pancreatic ductal adenocarcinoma

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.