3FUB

Crystal structure of GDNF-GFRalpha1 complex

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)
B	d3fubb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3fubd_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	automated matches	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	GDNF receptor-like	8038507	3000184	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GDNF receptor-like	8038507	3000184	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cystine-knot cytokines	8084508	3000846	SCOP2B (2022-06-29)
D	SCOP2 Family	Transforming growth factor (TGF)-beta	8084507	4003433	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Cystine-knot cytokines	8084508	3000846	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)
A	PF02351	e3fubA3	A: alpha superhelices	X: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like	H: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA	T: GDNF receptor	F: PF02351	ECOD (1.6)
C	PF02351	e3fubC3	A: alpha superhelices	X: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like	H: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA	T: GDNF receptor	F: PF02351	ECOD (1.6)
B	PF00019	e3fubB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00019	ECOD (1.6)
D	PF00019	e3fubD1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00019	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
D	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02351	GDNF/GAS1 domain (GDNF)	GDNF/GAS1 domain	This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons [2]. GDNF and neurturin promote neuronal surv ...	This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons [2]. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity [3].	Domain
B, D	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	GDNF family receptor alpha-1	molecular transducer activity signaling receptor activity cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding neurotrophin receptor activity	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development nervous system development cellular developmental process generation of neurons neurogenesis neuron differentiation cell differentiation cellular process kidney development renal system development cell migration cell motility plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development cellular component organization neuron development cellular component organization or biogenesis regulation of cellular process regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process organic substance metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation positive regulation of cellular process regulation of biological process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation regulation of metabolic process	protein-containing complex receptor complex cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle protein-containing complex receptor complex cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system plasma membrane protein complex membrane protein complex somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection extracellular region extracellular space endosome intracellular vesicle cytoplasmic vesicle late endosome multivesicular body vesicle
B, D	Glial cell line-derived neurotrophic factor	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity involved in axon guidance chemoattractant activity protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity involved in axon guidance chemoattractant activity protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding growth factor receptor binding glial cell-derived neurotrophic factor receptor binding identical protein binding protein homodimerization activity protein dimerization activity	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of biosynthetic process cellular biosynthetic process cellular metabolic process developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process multicellular organism development multicellular organismal process anatomical structure development sympathetic nervous system development autonomic nervous system development nervous system development system development spinal cord development central nervous system development dorsal spinal cord development positive regulation of biological process positive regulation of developmental process positive regulation of cell differentiation positive regulation of cellular process regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of catalytic activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity animal organ development embryonic organ development embryo development metanephros development kidney development renal system development kidney epithelium development renal vesicle morphogenesis epithelial cell differentiation regulation of epithelial cell differentiation metanephros morphogenesis regulation of epithelial cell differentiation involved in kidney development animal organ morphogenesis nephron development epithelium development tissue development positive regulation of epithelial cell differentiation nephron morphogenesis nephron epithelium morphogenesis regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis metanephric renal vesicle morphogenesis renal vesicle development positive regulation of epithelial cell differentiation involved in kidney development positive regulation of morphogenesis of an epithelium regulation of morphogenesis of an epithelium regulation of multicellular organismal process metanephric nephron development regulation of anatomical structure morphogenesis mesenchymal to epithelial transition involved in metanephros morphogenesis epithelial cell differentiation involved in kidney development nephron epithelium development regulation of multicellular organismal development morphogenesis of an epithelium mesenchymal to epithelial transition positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis metanephric nephron morphogenesis cell differentiation involved in metanephros development tissue morphogenesis anatomical structure morphogenesis kidney morphogenesis cell differentiation involved in kidney development specification of animal organ identity pattern specification process developmental induction animal organ formation regulation of animal organ morphogenesis regionalization positive regulation of animal organ morphogenesis anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process regulation of animal organ formation organ induction mesonephric epithelium development branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron tubule development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis ureteric bud development tube development mesonephros development morphogenesis of a branching structure mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development cellular component organization generation of neurons neurogenesis neuron differentiation neuron development cellular component organization or biogenesis cellular response to stimulus regulation of signaling response to stimulus cell surface receptor signaling pathway signaling semaphorin-plexin signaling pathway regulation of signal transduction cell communication regulation of semaphorin-plexin signaling pathway regulation of response to stimulus regulation of cell communication signal transduction system process smooth muscle contraction phasic smooth muscle contraction muscle contraction peristalsis muscle system process embryonic epithelial tube formation tube formation epithelial tube formation nephron tubule formation morphogenesis of embryonic epithelium mesonephric tubule formation embryonic morphogenesis ureteric bud formation adult locomotory behavior behavior adult behavior locomotory behavior negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling negative regulation of biological process regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway in absence of ligand apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of kidney development regulation of branching involved in ureteric bud morphogenesis regulation of morphogenesis of a branching structure positive regulation of branching involved in ureteric bud morphogenesis monoamine transport regulation of localization import into cell regulation of catecholamine uptake involved in synaptic transmission cellular localization nitrogen compound transport transport organic hydroxy compound transport catecholamine uptake dopamine transport localization dopamine uptake involved in synaptic transmission synaptic signaling catecholamine transport establishment of localization in cell regulation of dopamine uptake involved in synaptic transmission neurotransmitter reuptake regulation of neurotransmitter uptake trans-synaptic signaling regulation of transport catecholamine uptake involved in synaptic transmission regulation of neurotransmitter transport organic substance transport cell-cell signaling neurotransmitter transport establishment of localization chemical synaptic transmission amine transport anterograde trans-synaptic signaling neurotransmitter uptake regulation of amine transport synaptic transmission, dopaminergic dopamine uptake regulation of catecholamine secretion positive regulation of secretion by cell positive regulation of amine transport secretion by cell regulation of secretion by cell positive regulation of secretion signal release secretion positive regulation of catecholamine secretion export from cell dopamine secretion positive regulation of dopamine secretion regulation of secretion catecholamine secretion positive regulation of transport regulation of dopamine secretion stem cell development neural crest cell differentiation neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration cell migration mesenchymal cell differentiation cell motility neural crest cell migration neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process commissural neuron axon guidance axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance negative regulation of cellular metabolic process post-transcriptional regulation of gene expression negative regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process negative regulation of RNA metabolic process catabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process organic cyclic compound catabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process positive regulation of gene expression regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process membrane organization cell junction organization postsynapse organization synapse organization postsynaptic membrane organization parasympathetic nervous system development peripheral nervous system development postganglionic parasympathetic fiber development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation enteric nervous system development regulation of epithelial tube formation regulation of mesonephros development positive regulation of epithelial tube formation positive regulation of ureteric bud formation regulation of ureteric bud formation	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR037193	GDNF receptor alpha	Homologous Superfamily
A, C	IPR017372	Glial cell line-derived neurotrophic factor receptor, alpha 1/2	Family
A, C	IPR003438	Glial cell line-derived neurotrophic factor receptor	Family
A, C	IPR003503	Glial cell line-derived neurotrophic factor receptor, alpha 1	Family
A, C	IPR016017	GDNF/GAS1	Domain
B, D	IPR016649	Glial cell line-derived neurotrophic factor	Family
B, D	IPR029034	Cystine-knot cytokine	Homologous Superfamily
B, D	IPR047020	Glial cell line-derived neurotrophic factor, TGF-beta-like domain	Domain
B, D	IPR043401	Glial cell line-derived neurotrophic factor family	Family
B, D	IPR001839	Transforming growth factor-beta, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P39905	Hirschsprung disease congenital central hypoventilation syndrome phaeochromocytoma Huntington disease retinal degeneration ependymoma oligodendroglioma glioblastoma Parkinson disease malignant glioma status epilepticus childhood oligodendroglioma secondary Parkinson disease Neurologic Manifestations giant cell glioblastoma Hirschsprung disease congenital central hypoventilation syndrome phaeochromocytoma Huntington disease retinal degeneration ependymoma oligodendroglioma glioblastoma Parkinson disease malignant glioma status epilepticus childhood oligodendroglioma secondary Parkinson disease Neurologic Manifestations giant cell glioblastoma papillary ependymoma cocaine abuse myxopapillary ependymoma amphetamine abuse cellular ependymoma cocaine dependence mixed glioma adult oligodendroglioma oligoastrocytoma Hirschsprung disease, susceptibility to, 3 bowel dysfunction large cell medulloblastoma adrenal gland pheochromocytoma extra-adrenal sympathetic paraganglioma parkinsonian disorder autosomal recessive juvenile Parkinson disease 2 intestinal disease major depressive disorder cystic fibrosis adrenal medulla cancer drug-induced dyskinesia anaplastic ependymoma bipolar disorder juvenile Huntington disease schizophrenia congenital anomaly of kidney and urinary tract neurodegenerative disease osteosarcoma anaplastic oligodendroglioma glioma benign neoplasm of adrenal gland

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 R01GM133198.