4UMM

The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D [auth E]	SCOP2 Family	Nuclear receptor	8068355	4003622	SCOP2 (2022-06-29)
D [auth E]	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8068356	3000068	SCOP2 (2022-06-29)
E [auth F]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8032546	3001442	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8036574	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)
A	zf-C4	e4ummA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
D [auth E]	zf-C4	e4ummE1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
E [auth F]	Hormone_recep	e4ummF1	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)
F [auth G]	Hormone_recep	e4ummG1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E]	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
E [auth F]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ECR-USP	-	-	-
B [auth C]	5'-D(CPAPAPGPGPGPTPTPCPAPAPTPGPCP APCPTPTPGPTP)-3'	-	-	-
C [auth D]	5'-D(DGPAPCPAPAPGPTPGPCPAPTPTPGPDAP APCPCPCPTPT)-3'	-	-	-
D [auth E]	ECDYSONE RECEPTOR	nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding hormone binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding hormone binding ecdysone binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding sequence-specific DNA binding DNA binding nucleic acid binding	cellular response to stimulus cellular response to ecdysone response to organic substance response to ketone regulation of cellular process response to ecdysone intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to stimulus cellular response to ecdysone response to organic substance response to ketone regulation of cellular process response to ecdysone intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to sterol signal transduction cellular response to organic substance cellular response to ketone cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus ecdysone receptor-mediated signaling pathway regulation of biological process response to sterol response to endogenous stimulus response to alcohol biological regulation cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus steroid hormone mediated signaling pathway cellular response to alcohol response to chemical cellular response to lipid nuclear receptor signaling pathway cellular process intracellular steroid hormone receptor signaling pathway	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
E [auth F]	GENE REGULATION PROTEIN	nuclear steroid 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 DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding nuclear steroid 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 DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
F [auth G]	ECDYSONE RECEPTOR	nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding hormone binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding hormone binding ecdysone binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding sequence-specific DNA binding DNA binding nucleic acid binding	cellular response to stimulus cellular response to ecdysone response to organic substance response to ketone regulation of cellular process response to ecdysone intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to stimulus cellular response to ecdysone response to organic substance response to ketone regulation of cellular process response to ecdysone intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to sterol signal transduction cellular response to organic substance cellular response to ketone cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus ecdysone receptor-mediated signaling pathway regulation of biological process response to sterol response to endogenous stimulus response to alcohol biological regulation cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus steroid hormone mediated signaling pathway cellular response to alcohol response to chemical cellular response to lipid nuclear receptor signaling pathway cellular process intracellular steroid hormone receptor signaling pathway	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E]	IPR001723	Nuclear hormone receptor	Family
D [auth E]	IPR003069	Ecdysteroid receptor	Family
D [auth E]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
D [auth E]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
D [auth E]	IPR041889	Ecdysone receptor, ligand-binding domain	Domain
D [auth E]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
D [auth E]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
E [auth F]	IPR001723	Nuclear hormone receptor	Family
E [auth F]	IPR000003	Retinoid X receptor/HNF4	Family
E [auth F]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
E [auth F]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
F [auth G]	IPR001723	Nuclear hormone receptor	Family
F [auth G]	IPR003069	Ecdysteroid receptor	Family
F [auth G]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
F [auth G]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
F [auth G]	IPR041889	Ecdysone receptor, ligand-binding domain	Domain
F [auth G]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
F [auth G]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

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.