4UMM | pdb_00004umm

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)
F [auth G]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8036574	3001442	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8032546	3001442	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
D [auth E]	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
F [auth G]	ECDYSONE RECEPTOR	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 DNA binding sequence-specific DNA binding 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 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 DNA binding sequence-specific DNA binding 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 sterol 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	cellular response to stimulus cellular response to ecdysone ecdysone receptor signaling pathway 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 intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone cellular response to stimulus cellular response to ecdysone ecdysone receptor signaling pathway 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 intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to sterol signal transduction cellular response to ketone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of biological process response to sterol response to endogenous stimulus response to alcohol biological regulation response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to lipid cellular process nuclear receptor-mediated signaling pathway developmental process cellular developmental process cell differentiation 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 transcription by RNA polymerase II 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 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 regulation of macromolecule biosynthetic process macromolecule metabolic 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 biological process 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 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
E [auth F]	GENE REGULATION PROTEIN	nuclear receptor activity 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 ligand-modulated transcription factor activity DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding nuclear receptor activity 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 ligand-modulated transcription factor activity DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
D [auth E]	ECDYSONE RECEPTOR	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 DNA binding sequence-specific DNA binding 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 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 DNA binding sequence-specific DNA binding 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 sterol 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	cellular response to stimulus cellular response to ecdysone ecdysone receptor signaling pathway 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 intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone cellular response to stimulus cellular response to ecdysone ecdysone receptor signaling pathway 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 intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to sterol signal transduction cellular response to ketone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of biological process response to sterol response to endogenous stimulus response to alcohol biological regulation response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to lipid cellular process nuclear receptor-mediated signaling pathway developmental process cellular developmental process cell differentiation 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 transcription by RNA polymerase II 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 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 regulation of macromolecule biosynthetic process macromolecule metabolic 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 biological process 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 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
C [auth D]	5'-D(DGPAPCPAPAPGPTPGPCPAPTPTPGPDAP APCPCPCPTPT)-3'	-	-	-
B [auth C]	5'-D(CPAPAPGPGPGPTPTPCPAPAPTPGPCP APCPTPTPGPTP)-3'	-	-	-
A	ECR-USP	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
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
E [auth F]	IPR050274	Nuclear hormone receptor family NR2 subfamily	Family
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
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]	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
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