3F6K | pdb_00003f6k

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Vps10p beta-propeller domain-like	8052033	3002084	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sortilin C-terminal domain-like	8052044	3002085	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	Sortilin-Vps10	e3f6kA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 10-bladed	F: Sortilin-Vps10	ECOD (1.6)
A	Sortilin_C_2nd	e3f6kA3	A: few secondary structure elements	X: Sortilin C-terminal domain (From Topology)	H: Sortilin C-terminal domain (From Topology)	T: Sortilin C-terminal domain	F: Sortilin_C_2nd	ECOD (1.6)
A	Sortilin_C_1st	e3f6kA2	A: few secondary structure elements	X: Sortilin C-terminal domain (From Topology)	H: Sortilin C-terminal domain (From Topology)	T: Sortilin C-terminal domain	F: Sortilin_C_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.70.80	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)
A	3.30.60.270	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF15902	Sortilin, neurotensin receptor 3, (Sortilin-Vps10)	Sortilin, neurotensin receptor 3,	-	Repeat
A	PF15901	Sortilin, neurotensin receptor 3, C-terminal (Sortilin_C)	Sortilin, neurotensin receptor 3, C-terminal	Sortilin_C is the C-terminal cytoplasmic tail of sortilin, a Vps10p domain-containing family of proteins [1,2]. Most sortilin is expressed within intracellular compartments, where it chaperones diverse ligands, including proBDNF and acid hydrolases. ...	Sortilin_C is the C-terminal cytoplasmic tail of sortilin, a Vps10p domain-containing family of proteins [1,2]. Most sortilin is expressed within intracellular compartments, where it chaperones diverse ligands, including proBDNF and acid hydrolases. The sortilin cytoplasmic tail is homologous to mannose 6-phosphate receptor and is required for the intracellular trafficking of cargo proteins via interactions with distinct adaptor molecules [3,4]. In addition to mediating lysosomal targeting of specific acid hydrolases, the sortilin cytoplasmic tail also directs trafficking of BDNF to the secretory pathway in neurons, where it can be released in response to depolarisation to modulate cell survival and synaptic plasticity [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth N]	Neurotensin	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity G protein-coupled receptor binding neuropeptide receptor binding neuropeptide activity hormone activity neuropeptide hormone activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process negative regulation of metabolic process negative regulation of biological process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of tube diameter multicellular organismal process system process regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality blood circulation regulation of anatomical structure size 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 positive regulation of response to stimulus 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 response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling	cellular anatomical structure extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle transport vesicle intracellular vesicle endomembrane system cytoplasmic vesicle cytoplasm vesicle axon cellular anatomical structure extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle transport vesicle intracellular vesicle endomembrane system cytoplasmic vesicle cytoplasm vesicle axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon cell junction neuron projection terminus
A	Sortilin	molecular transducer activity neurotensin receptor activity, non-G protein-coupled transmembrane signaling receptor activity signaling receptor activity protein-containing complex binding binding retromer complex binding neurotrophin binding protein binding nerve growth factor binding growth factor binding enzyme binding nerve growth factor receptor activity neurotrophin receptor activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway developmental process fat cell differentiation regulation of developmental process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway developmental process fat cell differentiation regulation of developmental process cellular developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation negative regulation of fat cell differentiation cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of fat cell differentiation D-glucose import hexose transmembrane transport transport carbohydrate transport establishment of localization transmembrane transport localization D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport cellular localization endosome to lysosome transport intracellular transport lysosomal transport vesicle-mediated transport establishment of localization in cell vacuolar transport plasma membrane to endosome transport import into cell endocytosis 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 endosomal transport multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway maintenance of synapse structure cell junction maintenance cellular component organization cell junction organization cellular component maintenance cellular component organization or biogenesis synapse organization muscle structure development anatomical structure development striated muscle cell differentiation muscle cell differentiation myotube differentiation extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death post-Golgi vesicle-mediated transport Golgi to vacuole transport cytosolic transport Golgi to lysosome transport Golgi vesicle transport response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound multicellular organismal process ossification vesicle organization organelle organization cellular response to growth factor stimulus neurotrophin TRK receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus neurotrophin signaling pathway response to growth factor enzyme-linked receptor protein signaling pathway establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole protein targeting to lysosome intracellular protein localization protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein transport Golgi to endosome transport	cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope organelle membrane intracellular vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle cytoplasm vesicle cell surface cytosol Golgi cisterna membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna Golgi stack cell periphery plasma membrane lytic vacuole vacuole lysosome endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane early endosome endosome transport vesicle trans-Golgi network transport vesicle Golgi-associated vesicle vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane perinuclear region of cytoplasm endosome membrane cytoplasmic vesicle membrane vesicle membrane cerebellar climbing fiber to Purkinje cell synapse neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth N]	IPR008055	Neurotensin/neuromedin N	Family
A	IPR031777	Sortilin, C-terminal	Domain
A	IPR050310	VPS10-related sortilin family receptors	Family
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR006581	VPS10	Domain
A	IPR031778	Sortilin, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth N]	Pharos: P30990	Muscle Rigidity ovarian cancer schizophrenia chronic obstructive pulmonary disease head and neck cancer non-small cell lung carcinoma pituitary cancer attention deficit hyperactivity disorder, inattentive type lung cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor depressive disorder malignant ependymoma
A	Pharos: Q99523	cardiovascular disease coronary artery disease ovarian cancer tuberculosis abdominal aortic aneurysm cystic fibrosis glioblastoma lung cancer MALT lymphoma non-small cell lung carcinoma peripheral arterial disease astrocytic tumor Coronary Arteriosclerosis Down syndrome heart disease cardiovascular disease coronary artery disease ovarian cancer tuberculosis abdominal aortic aneurysm cystic fibrosis glioblastoma lung cancer MALT lymphoma non-small cell lung carcinoma peripheral arterial disease astrocytic tumor Coronary Arteriosclerosis Down syndrome heart disease malignant ependymoma medulloblastoma oligodendroglioma psoriasis atypical teratoid rhabdoid tumor esophageal adenocarcinoma large cell medulloblastoma malignant glioma myocardial infarction

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth N]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.