6CFN

Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6cfna_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6cfnb_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6cfnc_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6cfnd_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6cfne_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6cfnf_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6cfng_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6cfnh_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Glucocorticoid receptor DNA-binding domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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)	8068336	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	3000068	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068336	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	e6cfnA1	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	e6cfnB1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
C	zf-C4	e6cfnC1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
D	zf-C4	e6cfnD1	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	e6cfnE1	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	e6cfnF1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
G	zf-C4	e6cfnG1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
H	zf-C4	e6cfnH1	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)
C	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
D	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)
G	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
H	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, C, D, E A, B, C, D, E, F, G, H	PF00105	Double treble clef zinc finger, C4 type (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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Glucocorticoid receptor	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding steroid hormone binding steroid binding lipid binding hormone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding steroid hormone binding steroid binding lipid binding hormone binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding estrogen response element binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding protein binding TBP-class protein binding general transcription initiation factor binding nuclear receptor activity molecular transducer activity ligand-activated transcription factor activity signaling receptor activity nuclear steroid receptor activity nuclear glucocorticoid receptor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity Hsp90 protein binding heat shock protein binding RNA binding kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular process cell division cell cycle chromosome segregation cell cycle process apoptotic process cell death programmed cell death regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation cellular process cell division cell cycle chromosome segregation cell cycle process apoptotic process cell death programmed cell death regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of neuron apoptotic process positive regulation of cellular process regulation of neuron apoptotic process cellular response to stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to organic cyclic compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus developmental process multicellular organismal process epithelium development tube development mammary gland morphogenesis mammary gland development gland development animal organ development morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis gland morphogenesis mammary gland epithelium development anatomical structure development animal organ morphogenesis epithelial tube morphogenesis response to ketone cellular response to ketone cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid response to dexamethasone positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of miRNA transcription negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular 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 positive regulation of transcription by RNA polymerase II cellular component organization chromatin organization cellular component organization or biogenesis monosaccharide metabolic process gluconeogenesis regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process regulation of gluconeogenesis regulation of carbohydrate biosynthetic process glucose metabolic process glucocorticoid metabolic process steroid metabolic process lipid metabolic process cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to growth factor defense response response to stress inflammatory response neuroinflammatory response maternal behavior behavior parental behavior reproductive process multicellular organismal reproductive process reproductive behavior intracellular receptor signaling pathway signaling hormone-mediated signaling pathway intracellular signal transduction cell communication signal transduction nuclear receptor-mediated steroid hormone signaling pathway steroid hormone receptor signaling pathway nuclear receptor-mediated signaling pathway myeloid leukocyte differentiation cellular developmental process hemopoiesis macrophage differentiation cell development mononuclear cell differentiation nervous system development neurogenesis central nervous system development gliogenesis glial cell differentiation myeloid cell differentiation cell differentiation microglia differentiation system development leukocyte differentiation astrocyte differentiation adrenal gland development endocrine system development motor behavior regulation of steroid biosynthetic process regulation of hormone biosynthetic process regulation of hormone metabolic process regulation of lipid metabolic process lipid biosynthetic process regulation of glucocorticoid metabolic process regulation of biological quality regulation of glucocorticoid biosynthetic process steroid biosynthetic process hormone biosynthetic process steroid hormone biosynthetic process regulation of steroid hormone biosynthetic process regulation of hormone levels regulation of steroid metabolic process hormone metabolic process glucocorticoid biosynthetic process regulation of lipid biosynthetic process trans-synaptic signaling synaptic transmission, glutamatergic cell-cell signaling chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromatin chromosome cytoskeleton spindle microtubule cytoskeleton centrosome microtubule organizing center protein-containing complex synapse cell junction mitochondrion mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050200	Nuclear hormone receptor family NR3 subfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001409	Glucocorticoid receptor	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001723	Nuclear hormone receptor	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: P04150	glucocorticoid resistance endometriosis potassium deficiency disease psoriasis ocular hypertension atrial fibrillation 46,XX disorder of sex development melancholia ulcerative colitis schizophrenia hypokalemia cocaine abuse plasma cell myeloma endogenous depression cocaine dependence glucocorticoid resistance endometriosis potassium deficiency disease psoriasis ocular hypertension atrial fibrillation 46,XX disorder of sex development melancholia ulcerative colitis schizophrenia hypokalemia cocaine abuse plasma cell myeloma endogenous depression cocaine dependence obstructive lung disease bipolar disorder schizoaffective disorder hypertensive disorder prostate cancer sympathetic ophthalmia otitis externa exanthem keratitis ovarian cancer eye disease autoimmune hemolytic anemia pulmonary fibrosis Crohn disease temporal arteritis perennial allergic rhinitis bacterial conjunctivitis thyroiditis granuloma annulare blepharoconjunctivitis rhinitis trichinosis acute lymphoblastic leukemia polymyalgia rheumatica breast cancer scalp dermatosis dermatitis herpetiformis Diamond-Blackfan anemia vasomotor rhinitis seasonal allergic rhinitis multiple sclerosis alopecia areata proctitis anterior uveitis inherited aplastic anemia skin disease neurotic disorder epicondylitis aspiration pneumonitis pseudohermaphroditism iridocyclitis atopic conjunctivitis psoriatic arthritis juvenile idiopathic arthritis congenital adrenal hyperplasia synovitis atypical teratoid rhabdoid tumor pulmonary emphysema large cell medulloblastoma pancreatic intraductal papillary-mucinous carcinoma autoimmune thrombocytopenic purpura punctate epithelial keratoconjunctivitis lung cancer tendinitis rheumatic heart disease dacryocystitis tinea corporis hemorrhoid rosacea medulloblastoma depressive disorder tuberculosis Addison disease breast carcinoma dermatophytosis of groin and perianal area allergic asthma hyperaldosteronism Burkitt lymphoma schizophreniform disorder mood disorder ductal breast carcinoma in situ allergic rhinitis primary cutaneous T-cell lymphoma idiopathic acute eosinophilic pneumonia seborrheic dermatitis musculoskeletal system disease angioedema inflammatory bowel disease choroiditis eosinophilic esophagitis anxiety disorder intrinsic asthma chronic obstructive pulmonary disease erythema multiforme asthma iritis osteosarcoma atopic eczema contact dermatitis extrinsic allergic alveolitis autoimmune disease pulmonary eosinophilia lichen planus corneal ulcer systemic lupus erythematosus pemphigus B-cell chronic lymphocytic leukemia major depressive disorder tenosynovitis gout rheumatoid arthritis tinea pedis acquired thrombocytopenia pneumocystosis sarcoidosis adrenocortical insufficiency Hodgkins lymphoma bronchitis miliary tuberculosis uveitis allergic bronchopulmonary aspergillosis bursitis primitive neuroectodermal tumor mycosis fungoides ankylosing spondylitis chronic beryllium disease Sjogren syndrome nephrotic syndrome eosinophilic pneumonia aphthous stomatitis invasive ductal breast carcinoma Stevens-Johnson syndrome

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.