3BUK | pdb_00003buk

Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical 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	d3bukb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3buka_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3bukd1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 1	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d3bukd2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 2 and domain 3	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d3bukd4	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 4	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d3bukc1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 1	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d3bukc2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 2 and domain 3	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d3bukc4	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Low affinity neurotrophin receptor p75NTR, domain 4	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cystine-knot cytokines	8038795	3000846	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cystine-knot cytokines	8038795	3000846	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF receptor-like	8039412	3000971	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF receptor-like	8039413	3000971	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF receptor-like	8039414	3000971	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF receptor-like	8039415	3000971	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF receptor-like	8039412	3000971	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF receptor-like	8039414	3000971	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF receptor-like	8039415	3000971	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF receptor-like	8039413	3000971	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)
B	zf-C2H2	e3bukB1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-C2H2	ECOD (v294.1)
A	zf-C2H2	e3bukA1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-C2H2	ECOD (v294.1)
D	Ldl_recept_a	e3bukD1	A: a/b three-layered sandwiches	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (v294.1)
C	Ldl_recept_a	e3bukC1	A: a/b three-layered sandwiches	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (v294.1)

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)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
D	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
C	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00243	Nerve growth factor family (NGF)	Nerve growth factor family		Domain
C, D	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Neurotrophin-3	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity nerve growth factor receptor binding cytokine receptor binding neurotrophin receptor binding tumor necrosis factor receptor superfamily binding death receptor binding protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity nerve growth factor receptor binding cytokine receptor binding neurotrophin receptor binding tumor necrosis factor receptor superfamily binding death receptor binding chemoattractant activity	cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway response to nerve growth factor cellular process response to growth factor signal transduction positive chemotaxis chemotaxis positive regulation of locomotion regulation of response to external stimulus positive regulation of positive chemotaxis positive regulation of biological process response to external stimulus induction of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus regulation of positive chemotaxis positive regulation of response to external stimulus taxis regulation of response to stimulus response to chemical regulation of locomotion locomotion regulation of localization import into cell regulation of cellular component organization positive regulation of cellular component organization receptor internalization transport regulation of receptor internalization vesicle-mediated transport cellular component organization localization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis cell-cell signaling regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process regulation of neuron apoptotic process multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation trans-synaptic signaling modulation of chemical synaptic transmission chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway nerve development	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection extracellular region axon membrane-bounded organelle intracellular anatomical structure transport vesicle synapse intracellular vesicle somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection extracellular region axon membrane-bounded organelle intracellular anatomical structure transport vesicle synapse intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle organelle cell junction secretory vesicle cytoplasm vesicle exocytic vesicle
C, D	Tumor necrosis factor receptor superfamily member 16	small GTPase binding protein binding binding enzyme binding GTPase binding amyloid-beta binding peptide binding molecular transducer activity coreceptor activity signaling receptor activity neurotrophin binding nerve growth factor binding growth factor binding neurotrophin TRK receptor binding small GTPase binding protein binding binding enzyme binding GTPase binding amyloid-beta binding peptide binding molecular transducer activity coreceptor activity signaling receptor activity neurotrophin binding nerve growth factor binding growth factor binding neurotrophin TRK receptor binding neurotrophin TRKA receptor binding signaling receptor binding cytokine receptor binding neurotrophin receptor binding protein-containing complex binding calmodulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding identical protein binding transmembrane signaling receptor activity death receptor activity preprotein binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular homeostasis chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis intracellular chemical homeostasis intracellular glucose homeostasis multicellular organism development central nervous system development anatomical structure development nervous system development system development presynaptic modulation of chemical synaptic transmission regulation of programmed cell death positive regulation of apoptotic signaling pathway positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of mitochondrial depolarization negative regulation of membrane depolarization negative regulation of biological process mitochondrial depolarization regulation of membrane depolarization regulation of mitochondrial membrane potential membrane depolarization negative regulation of mitochondrial depolarization regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process extrinsic apoptotic signaling pathway epithelium development epidermis development molting cycle process hair cycle epidermis morphogenesis animal organ development morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle hair cycle process hair follicle morphogenesis regulation of neuron projection development regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis neuron differentiation cell differentiation negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization skeletal muscle cell differentiation skeletal muscle tissue development striated muscle tissue development muscle structure development skeletal muscle organ development muscle tissue development muscle organ development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress rhythmic process circadian regulation of gene expression circadian rhythm positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis endothelial cell proliferation angiogenesis negative regulation of endothelial cell proliferation tube morphogenesis epithelial cell proliferation blood vessel development negative regulation of cell population proliferation cell population proliferation negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis blood vessel morphogenesis tube development blood vessel endothelial cell proliferation involved in sprouting angiogenesis sprouting angiogenesis vasculature development circulatory system development regulation of endothelial cell proliferation regulation of cell population proliferation anatomical structure formation involved in morphogenesis regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion nerve development small GTPase-mediated signal transduction Rho protein signal transduction intracellular signal transduction intracellular signaling cassette artery development aorta development dorsal aorta development regulation of developmental process negative regulation of dendritic spine development regulation of dendritic spine development dendrite development dendritic spine development negative regulation of developmental process positive regulation of cell population proliferation positive regulation of neural precursor cell proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation response to fibroblast growth factor cellular response to growth factor stimulus negative regulation of signaling negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway negative regulation of fibroblast growth factor receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization regulation of animal organ morphogenesis regulation of odontogenesis of dentin-containing tooth regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis positive regulation of odontogenesis positive regulation of developmental process positive regulation of odontogenesis of dentin-containing tooth positive regulation of animal organ morphogenesis positive regulation of multicellular organismal process animal organ morphogenesis regulation of anatomical structure morphogenesis synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic negative regulation of programmed cell death negative regulation of apoptotic process fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation regulation of small GTPase mediated signal transduction regulation of intracellular signal transduction positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction positive regulation of small GTPase mediated signal transduction 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 response to alcohol response to oxygen-containing compound response to ethanol detection of external stimulus detection of stimulus detection of temperature stimulus response to external stimulus response to abiotic stimulus response to temperature stimulus detection of abiotic stimulus regulation of myelination regulation of nervous system development positive regulation of myelination axon ensheathment ensheathment of neurons positive regulation of nervous system process regulation of multicellular organismal development myelination cellular localization establishment of protein localization transport intracellular transport establishment of localization protein transport establishment of localization in cell intracellular protein transport positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade regulation of cell differentiation positive regulation of neuron differentiation positive regulation of cell differentiation regulation of neuron differentiation 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 positive regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process regulation of vasculature development negative regulation of blood vessel morphogenesis negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of multicellular organismal process reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of hair cycle regulation of hair follicle development negative regulation of hair follicle development positive regulation of synaptic transmission, cholinergic synaptic transmission, cholinergic regulation of synaptic transmission, cholinergic cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound response to amyloid-beta biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system presynapse synapse presynaptic membrane plasma membrane region synaptic membrane cytoplasm neuromuscular junction neuron spine neuron projection dendritic spine plasma membrane bounded cell projection cell projection postsynapse dendrite dendritic tree neuronal cell body membrane cell body membrane mitochondrion growth cone axon distal axon site of polarized growth membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cell leading edge leading edge membrane neuron projection membrane dendrite membrane cell projection membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse intracellular vesicle clathrin-coated endocytic vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle vesicle endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020408	Nerve growth factor-like	Family
A, B	IPR019846	Nerve growth factor conserved site	Conserved Site
A, B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B	IPR045815	Neutrophin-3, N-terminal	Domain
A, B	IPR002072	Nerve growth factor-related	Domain
A, B	IPR015578	Neurotrophin-3	Family
C, D	IPR000488	Death domain	Domain
C, D	IPR022325	Tumour necrosis factor receptor 16	Family
C, D	IPR041448	Tumor necrosis factor receptor member 16, transmembrane domain	Domain
C, D	IPR034046	Tumor necrosis factor receptor 16, N-terminal	Domain
C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
C, D	IPR052302	Neurotrophin receptor-related death domain-containing protein	Family
C, D	IPR001368	TNFR/NGFR cysteine-rich region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P20783	Down syndrome status epilepticus schizophrenia hearing loss disorder Nerve Degeneration diabetic autonomic neuropathy diabetic neuropathy diabetic polyneuropathy epilepsy with generalized tonic-clonic seizures major depressive disorder ovarian cancer sleep-wake disorder bipolar disorder medulloblastoma psoriasis Down syndrome status epilepticus schizophrenia hearing loss disorder Nerve Degeneration diabetic autonomic neuropathy diabetic neuropathy diabetic polyneuropathy epilepsy with generalized tonic-clonic seizures major depressive disorder ovarian cancer sleep-wake disorder bipolar disorder medulloblastoma psoriasis autism Sjogren syndrome breast cancer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.