3M9E | pdb_00003m9e

Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068354	3000068	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068354	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068354	3000068	SCOP2B (2022-06-29)
A	SCOP2 Family	Nuclear receptor	8068353	4003622	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068354	3000068	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	F5_F8_type_C	e3m9eF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
E	F5_F8_type_C	e3m9eE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
B	F5_F8_type_C	e3m9eB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
A	Ank,Ank_2	e3m9eA1	A: a/b three-layered sandwiches	X: Retrovirus capsid protein	H: Ubiquitin-related	T: Ubiquitin-like	F: Ank,Ank_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
B	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
A	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
C, D, G, H	DNA (5'-D(APTPTPGPAPCPCPTPCPAPGPCPTPGPAPGPGPTPCPAPAPT)-3')	-	-	-
A, B, E, F	Thyroid hormone receptor beta	thyroid hormone binding binding hormone 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 chromatin binding thyroid hormone binding binding hormone 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 chromatin binding transcription factor binding transcription coregulator binding protein binding transcription coactivator binding chromatin DNA binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity DNA-binding transcription factor activity signaling receptor activity ligand-modulated transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding enzyme binding identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid 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 regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid 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 negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process heart process multicellular organismal process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation regulation of multicellular organismal process heart contraction blood circulation developmental process cellular developmental process cell differentiation reproductive process negative regulation of female receptivity multicellular organismal reproductive process female mating behavior mating behavior behavior regulation of female receptivity reproductive behavior regulation of biological quality regulation of lipid metabolic process lipid metabolic process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis epithelium development tube development respiratory tube development lung epithelium development type I pneumocyte differentiation tissue development epithelial cell differentiation lung epithelial cell differentiation multicellular organism development lung cell differentiation lung development respiratory system development system development neutral lipid metabolic process regulation of triglyceride metabolic process triglyceride metabolic process glycerolipid metabolic process acylglycerol metabolic process regulation of cartilage development regulation of chondrocyte differentiation regulation of developmental process connective tissue development positive regulation of biological process regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process skeletal system development positive regulation of cell differentiation positive regulation of cellular process regulation of multicellular organismal development chondrocyte differentiation positive regulation of multicellular organismal process positive regulation of cartilage development cartilage development cellular response to stimulus 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 signal transduction nuclear receptor-mediated signaling pathway cellular response to hormone stimulus regulation of cholesterol metabolic process sterol metabolic process steroid metabolic process regulation of steroid metabolic process cholesterol metabolic process alcohol metabolic process secondary alcohol metabolic process regulation of small molecule metabolic process small molecule metabolic process embryonic organ development embryo development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation retinal cell apoptotic process neuron apoptotic process retinal cone cell apoptotic process apoptotic process cell death programmed cell death female courtship behavior courtship behavior mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of thyroid hormone receptor signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of thyroid hormone receptor signaling pathway regulation of signaling thyroid hormone receptor signaling pathway positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling response to thyroid hormone cellular response to thyroid hormone stimulus ossification positive regulation of ossification regulation of ossification regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II sensory organ development photoreceptor cell differentiation visual system development retina development in camera-type eye cell development neural retina development eye morphogenesis neurogenesis neuron differentiation retinal cone cell differentiation eye photoreceptor cell differentiation sensory system development photoreceptor cell development camera-type eye morphogenesis eye development eye photoreceptor cell development retinal cone cell development nervous system development camera-type eye photoreceptor cell differentiation generation of neurons retina morphogenesis in camera-type eye sensory organ morphogenesis neuron development camera-type eye development 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 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 membrane-enclosed lumen intracellular membraneless organelle 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 membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen membraneless organelle nuclear lumen

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	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A, B, E, F	IPR001723	Nuclear hormone receptor	Family
A, B, E, F	IPR001728	Thyroid hormone receptor	Family
A, B, E, F	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
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

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.