4XAJ | pdb_00004xaj

Crystal structure of human NR2E1/TLX

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8076829	3001442	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8076829	3001442	SCOP2B (2022-06-29)
D [auth B]	SCOP2 Family	Nuclear receptor ligand-binding domain	8076828	4001384	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Nuclear receptor ligand-binding domain	8076829	3001442	SCOP2 (2022-06-29)
E [auth D]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8076829	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	Hormone_recep_1	e4xajA2	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_1	ECOD (1.6)
A	SBP_bac_1_C	e4xajA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A	SBP_bac_1_N_1	e4xajA3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
B [auth C]	Hormone_recep_1	e4xajC2	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_1	ECOD (1.6)
B [auth C]	SBP_bac_1_C	e4xajC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B [auth C]	SBP_bac_1_N_1	e4xajC3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
D [auth B]	Hormone_recep_1	e4xajB1	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_1	ECOD (1.6)
D [auth B]	SBP_bac_1_C	e4xajB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
D [auth B]	SBP_bac_1_N_1	e4xajB3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
E [auth D]	Hormone_recep_1	e4xajD3	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_1	ECOD (1.6)
E [auth D]	SBP_bac_1_C	e4xajD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
B [auth C]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B [auth C]	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
D [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], D [auth B], E [auth D]	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A, B [auth C], D [auth B], E [auth D]	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, B [auth C], D [auth B], E [auth D]	Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding histone deacetylase binding protein binding enzyme binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding histone deacetylase binding protein binding enzyme binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding nucleic acid binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear steroid receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport multicellular organismal process regulation of cellular process localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation neuroblast proliferation cell population proliferation neural precursor cell proliferation forebrain development glial cell migration telencephalon glial cell migration cerebral cortex development telencephalon cell migration forebrain cell migration gliogenesis cell migration cell motility layer formation in cerebral cortex cerebral cortex cell migration head development animal organ development brain development cerebral cortex radially oriented cell migration pallium development anatomical structure morphogenesis central nervous system development anatomical structure formation involved in morphogenesis cerebral cortex radial glia-guided migration telencephalon development astrocyte cell migration forebrain generation of neurons central nervous system neuron differentiation cerebral cortex neuron differentiation forebrain neuron differentiation sensory organ development eye development retina development in camera-type eye visual system development camera-type eye development sensory system development cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization apoptotic process cell death programmed cell death regulation of stem cell proliferation positive regulation of cell population proliferation positive regulation of biological process positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation positive regulation of cellular process regulation of development, heterochronic regulation of timing of neuron differentiation regulation of timing of cell differentiation axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development central nervous system neuron development neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anterior commissure morphogenesis neuron development cell fate commitment somatic stem cell population maintenance maintenance of cell number stem cell population maintenance 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 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 olfactory lobe development olfactory bulb development cell cycle regulation of cell cycle positive regulation of cell cycle astrocyte differentiation regulation of neurogenesis regulation of gliogenesis regulation of astrocyte differentiation regulation of cell development regulation of nervous system development negative regulation of neurogenesis regulation of multicellular organismal process negative regulation of nervous system development regulation of multicellular organismal development regulation of glial cell differentiation negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation glial cell differentiation negative regulation of multicellular organismal process regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration angiogenesis tube morphogenesis regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration locomotion blood vessel development blood vessel morphogenesis tube development regulation of cell migration involved in sprouting angiogenesis sprouting angiogenesis vasculature development circulatory system development regulation of locomotion negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process behavior aggressive behavior regulation of vasculature development positive regulation of developmental process regulation of anatomical structure morphogenesis positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process biological process involved in intraspecies interaction between organisms social behavior sensory perception of light stimulus system process sensory perception nervous system process visual perception dentate gyrus development hippocampus development limbic system development regulation of neuron projection development regulation of cellular component organization dendrite development regulation of dendrite morphogenesis regulation of cell projection organization dendrite morphogenesis regulation of dendrite development regulation of plasma membrane bounded cell projection organization behavioral defense response fear response behavioral fear response response to stimulus defense response response to stress multicellular organismal response to stress negative regulation of cell population proliferation negative regulation of neural precursor cell proliferation regulation of neural precursor cell proliferation positive regulation of cell communication modulation of chemical synaptic transmission signaling cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication positive regulation of signaling positive regulation of nervous system development regulation of neuroblast proliferation positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of cell development positive regulation of neural precursor cell proliferation positive regulation of neuroblast proliferation amygdala development	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope periplasmic space intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C [auth Q], F [auth P]	Atrophin/grunge	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding protein binding binding DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding protein binding binding DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone deacetylase activity, hydrolytic mechanism histone modifying activity catalytic activity	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 developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification behavior inter-male aggressive behavior aggressive behavior sensory organ development eye development animal organ development visual system development sensory system development system development imaginal disc morphogenesis imaginal disc-derived wing morphogenesis metamorphosis wing disc morphogenesis imaginal disc development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis imaginal disc-derived wing vein morphogenesis appendage development post-embryonic appendage morphogenesis wing disc development instar larval or pupal development imaginal disc-derived appendage morphogenesis anatomical structure morphogenesis appendage morphogenesis imaginal disc-derived appendage development cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of ERBB signaling pathway regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II embryonic pattern specification embryo development muscle structure development somatic muscle development larval somatic muscle development larval development leg disc development leg disc morphogenesis imaginal disc-derived leg morphogenesis negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway	intracellular organelle polytene chromosome interband cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], D [auth B], E [auth D]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A, B [auth C], D [auth B], E [auth D]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, B [auth C], D [auth B], E [auth D]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A, B [auth C], D [auth B], E [auth D]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B [auth C], D [auth B], E [auth D]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B [auth C], D [auth B], E [auth D]	IPR050274	Nuclear hormone receptor family NR2 subfamily	Family
A, B [auth C], D [auth B], E [auth D]	IPR001723	Nuclear hormone receptor	Family
A, B [auth C], D [auth B], E [auth D]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B [auth C], D [auth B], E [auth D]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
C [auth Q], F [auth P]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C [auth Q], F [auth P]	IPR002951	Atrophin-like	Family
C [auth Q], F [auth P]	IPR017884	SANT domain	Domain
C [auth Q], F [auth P]	IPR001005	SANT/Myb domain	Domain
C [auth Q], F [auth P]	IPR000949	ELM2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], D [auth B], E [auth D]	Pharos: Q9Y466	astrocytic tumor large cell medulloblastoma oligodendroglioma subependymal giant cell astrocytoma bipolar disorder malignant ependymoma pilocytic astrocytoma bipolar I disorder medulloblastoma schizophrenia

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.