Annotations: 4NQA

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth H]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038695	3001442	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039031	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038695	3001442	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039081	3001442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039081	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)
G [auth H]	Hormone_recep	e4nqaH1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep	ECOD (1.6)
G [auth H]	zf-C4	e4nqaH2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
A	Hormone_recep	e4nqaA1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep	ECOD (1.6)
A	zf-C4	e4nqaA2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
H [auth I]	Hormone_recep	e4nqaI2	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep	ECOD (1.6)
H [auth I]	zf-C4	e4nqaI1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
B	Hormone_recep	e4nqaB1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep	ECOD (1.6)
B	zf-C4	e4nqaB2	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)
G [auth H]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (utative)
G [auth H]	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
A	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (utative)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
H [auth I]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.2.0)
H [auth I]	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.2.0)
B	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.2.0)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, G [auth H]	PF00105	Zinc finger, C4 type (two domains) (zf-C4)	Zinc finger, C4 type (two domains)	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, G [auth H]	PF11825	Nuclear/hormone receptor activator site AF-1 (Nuc_recep-AF1)	Nuclear/hormone receptor activator site AF-1	-	Family
A, G [auth H]	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
B, H [auth I]	PF00105	Zinc finger, C4 type (two domains) (zf-C4)	Zinc finger, C4 type (two domains)	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
B, H [auth I]	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
C, D, I [auth J], J [auth K]	PF08832	Steroid receptor coactivator (SRC-1)	Steroid receptor coactivator	This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding [1]. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.	Domain

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, G [auth H]	Retinoic acid receptor RXR-alpha	binding protein binding protein domain specific binding DNA binding domain binding DNA-binding transcription factor activity transcription regulator activity nucleic acid binding DNA binding double-stranded DNA binding organic cyclic compound binding heterocyclic compound binding enzyme binding identical protein binding LBD domain binding transcription factor binding nuclear receptor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding nuclear steroid receptor activity signaling receptor activity molecular transducer activity nuclear vitamin D receptor binding amide binding peptide binding sequence-specific DNA binding sequence-specific double-stranded DNA binding zinc ion binding ion binding cation binding metal ion binding transition metal ion binding	developmental process anatomical structure development cellular process cell differentiation cellular developmental process response to organic substance response to retinoic acid response to lipid response to chemical response to stimulus response to oxygen-containing compound	intracellular anatomical structure cytoplasm cytosol cellular anatomical entity mitochondrion organelle membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle nucleus nucleoplasm membrane-enclosed lumen nuclear lumen organelle lumen intracellular organelle lumen protein-containing complex receptor complex transcription regulator complex RNA polymerase II transcription regulator complex nuclear protein-containing complex
B, H [auth I]	Liver X nuclear receptor beta	signaling receptor binding binding protein binding apolipoprotein receptor binding apolipoprotein A-I receptor binding enzyme binding ATPase binding nucleic acid binding DNA binding chromatin binding chromatin DNA binding organic cyclic compound binding heterocyclic compound binding transcription factor binding nuclear receptor binding nuclear retinoic acid receptor binding nuclear retinoid X receptor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding zinc ion binding ion binding cation binding metal ion binding transition metal ion binding	cellular process cell differentiation developmental process cellular developmental process homeostatic process cholesterol homeostasis chemical homeostasis lipid homeostasis sterol homeostasis lipid localization cholesterol storage regulation of lipid storage regulation of cholesterol storage negative regulation of cholesterol storage negative regulation of lipid storage lipid storage regulation of localization macromolecule localization negative regulation of biological process regulation of biological process localization maintenance of location biological regulation regulation of lipid localization negative regulation of lipid localization metabolic process negative regulation of metabolic process gene expression regulation of gene expression negative regulation of macromolecule metabolic process negative regulation of gene expression regulation of metabolic process macromolecule metabolic process regulation of macromolecule metabolic process organic substance metabolic process macrophage derived foam cell differentiation regulation of macrophage derived foam cell differentiation negative regulation of macrophage derived foam cell differentiation regulation of cell differentiation negative regulation of cell differentiation negative regulation of cellular process regulation of developmental process regulation of cellular process negative regulation of developmental process foam cell differentiation positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of gene expression positive regulation of biological process cellular component organization cellular component assembly positive regulation of protein-containing complex assembly multicellular organismal process plasma lipoprotein particle assembly high-density lipoprotein particle assembly regulation of protein-containing complex assembly protein-containing complex organization cellular component biogenesis regulation of cellular component biogenesis positive regulation of cellular component biogenesis positive regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of multicellular organismal process positive regulation of multicellular organismal process protein-containing complex assembly protein-lipid complex assembly protein-lipid complex subunit organization plasma lipoprotein particle organization cellular component organization or biogenesis regulation of high-density lipoprotein particle assembly positive regulation of high-density lipoprotein particle assembly regulation of plasma lipoprotein particle levels positive regulation of lipid storage positive regulation of lipid localization positive regulation of catalytic activity positive regulation of molecular function regulation of catalytic activity regulation of lipoprotein lipase activity positive regulation of lipoprotein lipase activity regulation of hydrolase activity positive regulation of hydrolase activity regulation of lipase activity positive regulation of lipase activity positive regulation of triglyceride lipase activity regulation of molecular function response to external stimulus response to extracellular stimulus response to nutrient levels response to stimulus	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol nucleus nucleoplasm membrane-enclosed lumen nuclear lumen organelle membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle organelle lumen intracellular organelle lumen transcription regulator complex protein-containing complex RNA polymerase II transcription regulator complex nuclear protein-containing complex
C, D, I [auth J], J [auth K]	Nuclear receptor coactivator 2	signaling receptor binding binding protein binding transcription factor binding aryl hydrocarbon receptor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding nuclear receptor binding transcription coregulator activity transcription coactivator activity nuclear receptor coactivator activity transcription regulator activity protein dimerization activity protein domain specific binding	response to endogenous stimulus response to hormone cellular process response to organic substance cellular response to hormone stimulus response to chemical response to stimulus cellular response to stimulus cellular response to chemical stimulus cellular response to organic substance cellular response to endogenous stimulus response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine tissue development multicellular organismal process developmental process animal organ development positive regulation of biological process anatomical structure development regulation of biological process regulation of developmental process positive regulation of developmental process regulation of multicellular organismal process positive regulation of multicellular organismal process adipose tissue development connective tissue development biological regulation regulation of adipose tissue development positive regulation of adipose tissue development response to organonitrogen compound response to insulin cellular response to insulin stimulus response to peptide hormone regulation of response to stimulus regulation of cellular process cellular response to peptide hormone stimulus cellular response to organonitrogen compound regulation of cellular response to insulin stimulus response to peptide cellular response to peptide response to nitrogen compound cellular response to nitrogen compound response to oxygen-containing compound cellular response to oxygen-containing compound response to organic cyclic compound response to progesterone response to lipid response to steroid hormone response to ketone	intracellular anatomical structure cytoplasm cellular anatomical entity nucleus nucleoplasm nuclear body membrane-enclosed lumen nuclear lumen organelle membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle organelle lumen intracellular organelle lumen protein-containing complex transcription regulator complex RNA polymerase II transcription regulator complex nuclear protein-containing complex
E, K [auth L]	5'-D(TPAPAPGPGPTPCPAPCPTPTPCPAPGPGPTPCPA)-3'	none	none	none
F, L [auth M]	5'-D(TPAPTPGPAPCPCPTPGPAPAPGPTPGPAPCPCPT)-3'	none	none	none

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.