5VZ4

Receptor-growth factor crystal structure at 2.20 Angstrom resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d5vz4a_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	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	Cystine-knot cytokines	8070315	3000846	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	TGF_beta	e5vz4A1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
B	GDNF	e5vz4B1	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: GDNF	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain
B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Growth/differentiation factor 15	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity molecular function activator activity signaling receptor binding molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity growth factor activity	reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus homeostatic process eating behavior feeding behavior behavior multicellular organismal-level homeostasis response to dietary excess energy homeostasis cellular response to stimulus positive regulation of cell communication regulation of cellular process reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus homeostatic process eating behavior feeding behavior behavior multicellular organismal-level homeostasis response to dietary excess energy homeostasis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process positive regulation of signaling cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway SMAD protein signal transduction enzyme-linked receptor protein signaling pathway cell surface receptor protein tyrosine kinase signaling pathway glial cell-derived neurotrophic factor receptor signaling pathway positive regulation of cellular component organization regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion regulation of developmental process cellular developmental process cell-cell fusion muscle cell differentiation myotube differentiation cellular component organization positive regulation of developmental process muscle structure development cell differentiation anatomical structure development cellular component organization or biogenesis syncytium formation positive regulation of myoblast fusion developmental process myoblast fusion regulation of myoblast fusion positive regulation of syncytium formation by plasma membrane fusion syncytium formation by plasma membrane fusion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis striated muscle cell differentiation cell-cell signaling regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular response to nitrogen compound response to organic substance negative regulation of signaling response to peptide hormone negative regulation of biological process cellular response to growth hormone stimulus negative regulation of cell communication cellular response to endogenous stimulus regulation of growth hormone receptor signaling pathway response to hormone negative regulation of cellular process cellular response to organic substance cellular response to hormone stimulus growth hormone receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus response to organonitrogen compound cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound negative regulation of signal transduction response to growth hormone cellular response to chemical stimulus cellular response to organonitrogen compound negative regulation of growth hormone receptor signaling pathway response to chemical cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway regulation of multicellular organism growth regulation of growth regulation of developmental growth negative regulation of multicellular organism growth developmental growth negative regulation of developmental process growth multicellular organism growth negative regulation of developmental growth negative regulation of growth regulation of multicellular organismal process negative regulation of multicellular organismal process	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular space membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular space vesicle extracellular membrane-bounded organelle nucleus
B	GDNF family receptor alpha-like	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity cytokine receptor activity immune receptor activity glial cell-derived neurotrophic factor receptor activity protein tyrosine kinase binding protein binding binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding	reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus homeostatic process eating behavior feeding behavior behavior multicellular organismal-level homeostasis response to dietary excess energy homeostasis cellular response to stimulus positive regulation of cell communication regulation of cellular process reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus homeostatic process eating behavior feeding behavior behavior multicellular organismal-level homeostasis response to dietary excess energy homeostasis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process positive regulation of signaling 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 cell surface receptor signaling pathway 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 stress-activated protein kinase signaling cascade cellular response to stress response to stress developmental process multicellular organism development anatomical structure development nervous system development system development cell surface receptor protein tyrosine kinase signaling pathway glial cell-derived neurotrophic factor receptor signaling pathway enzyme-linked receptor protein signaling pathway regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process	protein-containing complex receptor complex anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular organelle protein-containing complex receptor complex anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A	IPR001839	Transforming growth factor-beta, C-terminal	Domain
A	IPR015615	Transforming growth factor-beta-related	Family
B	IPR037193	GDNF receptor alpha	Homologous Superfamily
B	IPR003438	Glial cell line-derived neurotrophic factor receptor	Family
B	IPR016017	GDNF/GAS1	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q99988	melanoma sideroblastic anemia Weight Gain coronary artery disease prostate cancer congestive heart failure mouth disease breast carcinoma subependymal giant cell astrocytoma lung adenocarcinoma atypical teratoid rhabdoid tumor malignant ependymoma chronic obstructive pulmonary disease myocardial ischemia nephrosclerosis melanoma sideroblastic anemia Weight Gain coronary artery disease prostate cancer congestive heart failure mouth disease breast carcinoma subependymal giant cell astrocytoma lung adenocarcinoma atypical teratoid rhabdoid tumor malignant ependymoma chronic obstructive pulmonary disease myocardial ischemia nephrosclerosis ovarian cancer gastric carcinoma glioblastoma sarcoidosis heart disease systemic lupus erythematosus hepatocellular carcinoma invasive ductal breast carcinoma lung cancer breast cancer malignant glioma nasopharyngeal carcinoma cutaneous melanoma non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic ductal adenocarcinoma gastroesophageal reflux disease Hashimoto thyroiditis heart failure ulcerative colitis hypertensive disorder juvenile dermatomyositis malignant colon neoplasm digestive system cancer osteosarcoma esophageal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis
B	Pharos: Q6UXV0	Malignant neoplasm of breast

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.