9BD8 | pdb_00009bd8

ApoB 100 beta barrel bound to LDLR beta propeller

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	YWTD domain-like	8034029	3000494	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	HSP20	e9bd8B01	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase	T: Helical bundle in Hef helicase	F: HSP20	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01347	Lipoprotein amino terminal region (Vitellogenin_N)	Lipoprotein amino terminal region	-	Repeat
A	PF06448	Domain of Unknown Function (DUF1081) (DUF1081)	Domain of Unknown Function (DUF1081)	-	Family
B	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Apolipoprotein B-100	binding phospholipid binding lipid binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding binding phospholipid binding lipid binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding enzyme binding lipase binding low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation neutral lipid metabolic process triglyceride metabolic process primary metabolic process metabolic process cellular process glycerolipid metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation neutral lipid metabolic process triglyceride metabolic process primary metabolic process metabolic process cellular process glycerolipid metabolic process triglyceride mobilization acylglycerol metabolic process lipid metabolic process fertilization regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation 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 positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process localization transport macromolecule localization lipid localization cholesterol transport lipid transport sterol transport organic hydroxy compound transport establishment of localization multicellular organismal 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 embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development establishment of protein localization protein transport lipoprotein transport intracellular protein localization lipoprotein localization nervous system development cholesterol efflux very-low-density lipoprotein particle assembly plasma lipoprotein particle organization protein-containing complex organization protein-lipid complex organization regulation of plasma lipoprotein particle levels cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly plasma lipoprotein particle assembly protein-lipid complex assembly cellular component organization or biogenesis lipoprotein biosynthetic process lipoprotein metabolic process protein metabolic process low-density lipoprotein particle remodeling protein-containing complex remodeling plasma lipoprotein particle remodeling protein-lipid complex remodeling regulation of localization lipid storage positive regulation of lipid localization regulation of lipid storage regulation of lipid localization nutrient storage positive regulation of lipid storage sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process small molecule metabolic process regulation of developmental process cellular developmental process macrophage derived foam cell differentiation regulation of cell differentiation positive regulation of developmental process foam cell differentiation positive regulation of cell differentiation cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation sperm motility cilium movement involved in cell motility cilium or flagellum-dependent cell motility cilium-dependent cell motility flagellated sperm motility microtubule-based movement microtubule-based process cilium movement cell motility cellular localization establishment of localization in cell cholesterol storage positive regulation of cholesterol storage regulation of cholesterol storage lipid catabolic process catabolic process neutral lipid catabolic process glycerolipid catabolic process acylglycerol catabolic process triglyceride catabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus cellular response to stimulus cellular response to lipoprotein particle stimulus protein catabolic process lipoprotein catabolic process macromolecule catabolic process regulation of cholesterol biosynthetic process regulation of steroid biosynthetic process regulation of cholesterol metabolic process regulation of lipid metabolic process lipid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process small molecule biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process sterol biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process regulation of lipid biosynthetic process post-embryonic development plasma lipoprotein particle clearance low-density lipoprotein particle clearance	protein-containing complex cellular anatomical structure extracellular region plasma lipoprotein particle mature chylomicron extracellular space lipoprotein particle chylomicron protein-lipid complex membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle protein-containing complex cellular anatomical structure extracellular region plasma lipoprotein particle mature chylomicron extracellular space lipoprotein particle chylomicron protein-lipid complex 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 membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle cytosol endoplasmic reticulum smooth endoplasmic reticulum endomembrane system endoplasmic reticulum exit site membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen chylomicron remnant endosome membrane endosome somatodendritic compartment cell body neuronal cell body lytic vacuole vacuolar lumen vacuole lysosomal lumen lysosome cell periphery plasma membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane early endosome low-density lipoprotein particle lipid droplet membraneless organelle intracellular membraneless organelle intermediate-density lipoprotein particle triglyceride-rich plasma lipoprotein particle endocytic vesicle lumen endosome lumen very-low-density lipoprotein particle
B	Low-density lipoprotein receptor	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 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	multicellular organismal process catabolic process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic 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 multicellular organismal process catabolic process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic 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 biosynthetic process regulation of cellular 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 positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process macromolecule localization 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 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 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 regulation of protein metabolic process negative regulation of metabolic process negative regulation of biological process negative regulation of cellular 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 cellular response to low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle 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 diterpenoid metabolic process retinoid metabolic process terpenoid metabolic process isoprenoid metabolic process astrocyte differentiation negative regulation of astrocyte activation regulation of cell activation regulation of neurogenesis regulation of cell differentiation 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 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 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 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 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 lipoprotein metabolic process lipoprotein catabolic 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 negative regulation of supramolecular fiber organization cellular component organization or biogenesis 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 phospholipid 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 phosphorus metabolic process glycerophospholipid catabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane 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 cellular anatomical structure cell surface membrane plasma membrane 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	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR015255	Vitellinogen, open beta-sheet	Domain
A	IPR015819	Lipid transport protein, beta-sheet shell	Homologous Superfamily
A	IPR022176	Apolipoprotein B100 C-terminal	Domain
A	IPR052418	Apolipoprotein B	Family
A	IPR011030	Lipovitellin-phosvitin complex, superhelical domain	Homologous Superfamily
A	IPR015816	Vitellinogen, beta-sheet N-terminal	Homologous Superfamily
A	IPR001747	Vitellogenin, N-terminal	Domain
A	IPR009454	Lipid transport, open beta-sheet	Domain
A	IPR015817	Vitellinogen, open beta-sheet, subdomain 1	Homologous Superfamily
B	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
B	IPR000033	LDLR class B repeat	Repeat
B	IPR001881	EGF-like calcium-binding domain	Domain
B	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
B	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
B	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
B	IPR000742	EGF-like domain	Domain
B	IPR051221	Low-density lipoprotein receptor-related	Family
B	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04114	familial hypobetalipoproteinemia 1 Hypobetalipoproteinemia, Familial, Apolipoprotein B familial hypercholesterolemia abetalipoproteinemia hypertriglyceridemia familial isolated deficiency of vitamin E hypercholesterolemia, autosomal dominant, type B Behcet disease atherosclerosis cardiovascular disease coronary artery disease metabolic syndrome X type 2 diabetes mellitus fatty liver disease hypercholesterolemia, familial, 1 familial hypobetalipoproteinemia 1 Hypobetalipoproteinemia, Familial, Apolipoprotein B familial hypercholesterolemia abetalipoproteinemia hypertriglyceridemia familial isolated deficiency of vitamin E hypercholesterolemia, autosomal dominant, type B Behcet disease atherosclerosis cardiovascular disease coronary artery disease metabolic syndrome X type 2 diabetes mellitus fatty liver disease hypercholesterolemia, familial, 1 atrial fibrillation cerebrovascular disorder inborn carbohydrate metabolic disorder invasive ductal breast carcinoma myocardial infarction ductal breast carcinoma in situ pancreatic ductal adenocarcinoma exocrine pancreatic carcinoma psoriasis familial hyperlipidemia gastroesophageal reflux disease inborn errors of metabolism colorectal cancer cystic fibrosis obesity disorder peripheral nervous system disease heart disease hyperlipidemia hypertensive disorder hypolipoproteinemia inherited lipid metabolism disorder osteosarcoma peripheral neuropathy
B	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