4N7E | pdb_00004n7e

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469

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	SCOP2 Family	Sortilin-like	8044711	4004094	SCOP2 (2022-06-29)
A	SCOP2 Family	Sortilin C-terminal domain-like	8052043	4007575	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Vps10p beta-propeller domain-like	8052033	3002084	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sortilin C-terminal domain-like	8052044	3002085	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	Ribonuclease_3	e4n7eA4	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Ribonuclease_3	ECOD (v294.1)

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
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 cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization 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 protein targeting establishment of protein localization to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein targeting to lysosome protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole 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
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
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

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.