3SO6

Crystal structure of the LDL receptor tail in complex with autosomal recessive hypercholesterolemia PTB domain

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	Phosphotyrosine-binding domain (PTB)	8077854	4002427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PH domain-like	8077855	3000134	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	PF00640	e3so6A1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF00640	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00640	Phosphotyrosine interaction domain (PTB/PID) (PID)	Phosphotyrosine interaction domain (PTB/PID)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LDL receptor adaptor protein	clathrin binding protein binding binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity amide binding amyloid-beta binding peptide binding protein-containing complex binding AP-2 adaptor complex binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding clathrin binding protein binding binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity amide binding amyloid-beta binding peptide binding protein-containing complex binding AP-2 adaptor complex binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding AP-1 adaptor complex binding ion binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding cargo adaptor activity clathrin adaptor activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding signaling receptor complex adaptor activity	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport regulation of vascular associated smooth muscle cell proliferation regulation of biological process cell population proliferation regulation of cellular process positive regulation of vascular associated smooth muscle cell proliferation localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport regulation of vascular associated smooth muscle cell proliferation regulation of biological process cell population proliferation regulation of cellular process positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation biological regulation positive regulation of biological process smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation positive regulation of cellular process sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process organic substance metabolic process small molecule metabolic process metabolic process lipid metabolic process multicellular organismal process positive regulation of low-density lipoprotein particle clearance regulation of plasma lipoprotein particle levels regulation of low-density lipoprotein particle clearance positive regulation of lipoprotein particle clearance plasma lipoprotein particle clearance regulation of lipoprotein particle clearance positive regulation of multicellular organismal process regulation of multicellular organismal process low-density lipoprotein particle clearance regulation of localization regulation of receptor-mediated endocytosis involved in cholesterol transport positive regulation of intracellular lipid transport positive regulation of intracellular cholesterol transport regulation of intracellular cholesterol transport positive regulation of endocytosis establishment of localization in cell sterol transport positive regulation of receptor-mediated endocytosis regulation of intracellular transport regulation of sterol transport intracellular lipid transport organic substance transport intracellular transport lipid transport positive regulation of lipid transport cholesterol transport cellular localization regulation of cellular component organization positive regulation of cellular component organization positive regulation of sterol transport regulation of intracellular sterol transport intracellular cholesterol transport regulation of lipid transport positive regulation of receptor-mediated endocytosis involved in cholesterol transport organic hydroxy compound transport intracellular sterol transport cellular component organization receptor-mediated endocytosis involved in cholesterol transport positive regulation of intracellular transport cellular component organization or biogenesis positive regulation of intracellular sterol transport regulation of cholesterol transport regulation of endocytosis positive regulation of cholesterol transport regulation of transport regulation of receptor-mediated endocytosis regulation of intracellular lipid transport lipid localization positive regulation of lipid localization regulation of vesicle-mediated transport positive regulation of transport regulation of cellular localization regulation of lipid localization macromolecule localization organonitrogen compound metabolic process protein metabolic process macromolecule metabolic process amyloid precursor protein metabolic process protein localization protein localization to cell periphery regulation of protein localization protein localization to plasma membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane cellular macromolecule localization regulation of protein localization to plasma membrane regulation of protein localization to membrane cellular response to stimulus response to organic substance cellular response to chemical stimulus response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus cellular response to organic substance	cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle early endosome endosome intracellular vesicle cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle recycling endosome axon cell projection neuron projection plasma membrane bounded cell projection cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane polymeric cytoskeletal fiber neurofilament intermediate filament cytoskeleton cytoskeleton intracellular non-membrane-bounded organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle
B [auth Q]	Low-density lipoprotein receptor	amide binding amyloid-beta binding binding peptide binding molecular adaptor activity identical protein binding protein binding virus receptor activity exogenous protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding amide binding amyloid-beta binding binding peptide binding molecular adaptor activity identical protein binding protein binding virus receptor activity exogenous protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding lipoprotein particle receptor activity cargo receptor activity very-low-density lipoprotein particle receptor activity enzyme binding protease binding clathrin heavy chain binding clathrin binding low-density lipoprotein particle receptor activity lipoprotein particle binding protein-containing complex binding protein-lipid complex binding low-density lipoprotein particle binding	cellular catabolic process multicellular organismal process catabolic process amyloid-beta clearance by cellular catabolic process cellular metabolic process metabolic process cellular process amyloid-beta clearance regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation cellular catabolic process multicellular organismal process catabolic process amyloid-beta clearance by cellular catabolic process cellular metabolic process metabolic process cellular process amyloid-beta clearance regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport regulation of cellular process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic 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 biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process macromolecule localization organic substance transport phospholipid transport lipid localization lipid transport organophosphate ester transport cholesterol transport sterol transport organic hydroxy compound transport plasma lipoprotein particle clearance regulation of plasma lipoprotein particle levels developmental process blood vessel morphogenesis tube development artery development vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development artery morphogenesis blood vessel development system development regulation of cholesterol metabolic process organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process regulation of steroid metabolic process regulation of lipid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process regulation of primary metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process regulation of small molecule metabolic process small molecule metabolic process lipid metabolic process response to nutrient levels response to caloric restriction organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process negative regulation of biological process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance regulation of multicellular organismal process low-density lipoprotein particle clearance negative regulation of multicellular organismal process intestinal lipid absorption digestion system process intestinal absorption digestive system process intestinal cholesterol absorption lipid digestion cellular response to stimulus response to organic substance response to endogenous stimulus response to organonitrogen compound response to lipoprotein particle response to nitrogen compound cellular response to low-density lipoprotein particle stimulus response to chemical cellular response to lipoprotein particle stimulus cellular localization intracellular lipid transport intracellular cholesterol transport intracellular transport intracellular sterol transport establishment of localization in cell receptor-mediated endocytosis involved in cholesterol transport receptor-mediated endocytosis cholesterol import astrocyte differentiation negative regulation of astrocyte activation regulation of cell activation regulation of cell differentiation regulation of neurogenesis astrocyte activation glial cell development regulation of astrocyte differentiation regulation of cell development gliogenesis cell differentiation nervous system development negative regulation of gliogenesis negative regulation of glial cell differentiation central nervous system development negative regulation of response to external stimulus negative regulation of defense response glial cell activation neuroinflammatory response cellular developmental process regulation of developmental process negative regulation of inflammatory response cell development regulation of gliogenesis regulation of nervous system development neurogenesis negative regulation of neurogenesis astrocyte development regulation of neuroinflammatory response negative regulation of cellular process negative regulation of nervous system development negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of response to stimulus negative regulation of developmental process cell activation regulation of glial cell differentiation negative regulation of astrocyte differentiation negative regulation of cell activation negative regulation of cell development glial cell differentiation regulation of astrocyte activation negative regulation of neuroinflammatory response regulation of macrophage activation regulation of leukocyte activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response regulation of immune system process negative regulation of microglial cell activation negative regulation of immune system process immune system process microglial cell activation regulation of microglial cell activation negative regulation of leukocyte activation negative regulation of macrophage activation sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis neutral lipid metabolic process neutral lipid biosynthetic process regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process lipid biosynthetic process acylglycerol biosynthetic process triglyceride metabolic process triglyceride biosynthetic process positive regulation of lipid metabolic process regulation of triglyceride biosynthetic process positive regulation of triglyceride biosynthetic process glycerolipid biosynthetic process positive regulation of lipid biosynthetic process cellular lipid metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process acylglycerol metabolic process behavior learning or memory long-term memory nervous system process cognition memory high-density lipoprotein particle clearance regulation of protein catabolic process in the vacuole positive regulation of protein metabolic process lysosomal protein catabolic process macromolecule catabolic process positive regulation of lysosomal protein catabolic process organonitrogen compound catabolic process protein catabolic process in the vacuole protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of lysosomal protein catabolic process positive regulation of protein catabolic process in the vacuole organic substance catabolic process regulation of protein catabolic process regulation of signaling negative regulation of signaling signaling regulation of receptor recycling negative regulation of receptor recycling receptor recycling receptor metabolic process response to lipid response to fatty acid response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to fatty acid cellular response to chemical stimulus cellular response to lipid cellular response to organic substance lipoprotein metabolic process lipoprotein catabolic process negative regulation of cellular metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of cellular component organization negative regulation of amyloid fibril formation regulation of amyloid fibril formation amyloid fibril formation cellular component organization cellular component organization or biogenesis negative regulation of supramolecular fiber organization negative regulation of cellular component organization regulation of supramolecular fiber organization supramolecular fiber organization phospholipid catabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process cellular lipid catabolic process phospholipid metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphatidylcholine metabolic process phosphorus metabolic process regulation of phospholipid catabolic process lipid catabolic process regulation of phosphatidylcholine metabolic process regulation of phospholipid metabolic process regulation of lipid catabolic process phosphatidylcholine catabolic process organophosphate metabolic process regulation of phosphatidylcholine catabolic process regulation of cellular catabolic process regulation of phosphorus metabolic process glycerophospholipid catabolic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex receptor complex Golgi apparatus endosome membrane endosome sorting endosome somatodendritic compartment endolysosome membrane lytic vacuole endolysosome lysosome vacuolar membrane vacuole lytic vacuole membrane lysosomal membrane early endosome PCSK9-LDLR complex low-density lipoprotein particle extracellular region plasma lipoprotein particle extracellular space lipoprotein particle protein-lipid complex late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR006020	PTB/PI domain	Domain
B [auth Q]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth Q]	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
B [auth Q]	IPR000033	LDLR class B repeat	Repeat
B [auth Q]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth Q]	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B [auth Q]	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
B [auth Q]	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
B [auth Q]	IPR000742	EGF-like domain	Domain
B [auth Q]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B [auth Q]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth Q]	Pharos: P01130	familial hypercholesterolemia Dyslipidemias abdominal aortic aneurysm non-alcoholic fatty liver disease coronary artery disease obesity disorder Q fever amyotrophic lateral sclerosis type 1 hyperplasia atherosclerosis ovarian cancer psoriasis sinusitis glioblastoma invasive ductal breast carcinoma familial hypercholesterolemia Dyslipidemias abdominal aortic aneurysm non-alcoholic fatty liver disease coronary artery disease obesity disorder Q fever amyotrophic lateral sclerosis type 1 hyperplasia atherosclerosis ovarian cancer psoriasis sinusitis glioblastoma invasive ductal breast carcinoma arteriosclerosis disorder lung adenocarcinoma atypical teratoid rhabdoid tumor malignant pancreatic neoplasm cystic fibrosis pancreatic ductal adenocarcinoma fatty liver disease Sjogren syndrome heart disease type 2 diabetes mellitus lung cancer breast cancer medulloblastoma congestive heart failure non-small cell lung carcinoma osteosarcoma ductal breast carcinoma in situ peripheral arterial disease exocrine pancreatic carcinoma familial hyperlipidemia sarcoidosis Gaucher disease spina bifida hydrolethalus syndrome ulcerative colitis hyperlipidemia alcohol abuse lung carcinoma carotid artery disease 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 R01GM133198.