MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
1B68	2.0	APOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT
1BZ4	1.85	APOLIPOPROTEIN E3 (APO-E3), TRUNCATION MUTANT 165
1EA8	1.95	Apolipoprotein E3 22kD fragment LYS146GLU mutant
1GS9	1.7	Apolipoprotein E4, 22k domain
1H7I	1.9	Apolipoprotein E3 22kD fragment LYS146GLN mutant
1LE2	3.0	STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E
1LE4	2.5	STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E
1LPE	2.25	THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF HUMAN APOLIPOPROTEIN E
1NFN	1.8	APOLIPOPROTEIN E3 (APOE3)
1NFO	2.0	APOLIPOPROTEIN E2 (APOE2, D154A MUTATION)
1OEF		PEPTIDE OF HUMAN APOE RESIDUES 263-286, NMR, 5 STRUCTURES AT PH 4.8, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90
1OEG		PEPTIDE OF HUMAN APOE RESIDUES 267-289, NMR, 5 STRUCTURES AT PH 6.0, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90
1OR2	2.5	APOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165
1OR3	1.73	APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165
2KC3		NMR solution structure of complete receptor binding domain of human apolipoprotein E
2KNY		Fusion construct of CR17 from LRP-1 and ApoE residues 130-149
2L7B		NMR Structure of full length apoE3
6IWB	2.5	Crystal structure of a computationally designed protein (LD3) in complex with BCL-2
6NCN	1.82	Fragment-based Discovery of an apoE4 Stabilizer
6NCO	1.707	Fragment-based Discovery of an apoE4 Stabilizer
7FCR	1.4	Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
7FCS	1.6	Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
7UVJ	1.99	Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2

GO term

GO ontology	GO term	GO description
Biological Process	GO:0097113	AMPA glutamate receptor clustering
Biological Process	GO:0007186	G protein-coupled receptor signaling pathway
Biological Process	GO:0097114	NMDA glutamate receptor clustering
Biological Process	GO:0042982	amyloid precursor protein metabolic process
Biological Process	GO:0048844	artery morphogenesis
Biological Process	GO:0019934	cGMP-mediated signaling
Biological Process	GO:0006707	cholesterol catabolic process
Biological Process	GO:0033344	cholesterol efflux
Biological Process	GO:0042632	cholesterol homeostasis
Biological Process	GO:0008203	cholesterol metabolic process
Biological Process	GO:0034382	chylomicron remnant clearance
Biological Process	GO:0007010	cytoskeleton organization
Biological Process	GO:0055089	fatty acid homeostasis
Biological Process	GO:0010467	gene expression
Biological Process	GO:0034380	high-density lipoprotein particle assembly
Biological Process	GO:0034384	high-density lipoprotein particle clearance
Biological Process	GO:0034375	high-density lipoprotein particle remodeling
Biological Process	GO:0071831	intermediate-density lipoprotein particle clearance
Biological Process	GO:0006874	intracellular calcium ion homeostasis
Biological Process	GO:0046907	intracellular transport
Biological Process	GO:0010877	lipid transport involved in lipid storage
Biological Process	GO:0042158	lipoprotein biosynthetic process
Biological Process	GO:0042159	lipoprotein catabolic process
Biological Process	GO:0035641	locomotory exploration behavior
Biological Process	GO:0015909	long-chain fatty acid transport
Biological Process	GO:0007616	long-term memory
Biological Process	GO:0034374	low-density lipoprotein particle remodeling
Biological Process	GO:0051651	maintenance of location in cell
Biological Process	GO:0032438	melanosome organization
Biological Process	GO:0043407	negative regulation of MAP kinase activity
Biological Process	GO:1905907	negative regulation of amyloid fibril formation
Biological Process	GO:1902430	negative regulation of amyloid-beta formation
Biological Process	GO:0030195	negative regulation of blood coagulation
Biological Process	GO:0043537	negative regulation of blood vessel endothelial cell migration
Biological Process	GO:0090090	negative regulation of canonical Wnt signaling pathway
Biological Process	GO:0045541	negative regulation of cholesterol biosynthetic process
Biological Process	GO:0090370	negative regulation of cholesterol efflux
Biological Process	GO:0061000	negative regulation of dendritic spine development
Biological Process	GO:1902951	negative regulation of dendritic spine maintenance
Biological Process	GO:0010596	negative regulation of endothelial cell migration
Biological Process	GO:0001937	negative regulation of endothelial cell proliferation
Biological Process	GO:0010629	negative regulation of gene expression
Biological Process	GO:0050728	negative regulation of inflammatory response
Biological Process	GO:0051055	negative regulation of lipid biosynthetic process
Biological Process	GO:1903001	negative regulation of lipid transport across blood-brain barrier
Biological Process	GO:1900272	negative regulation of long-term synaptic potentiation
Biological Process	GO:0043524	negative regulation of neuron apoptotic process
Biological Process	GO:1901215	negative regulation of neuron death
Biological Process	GO:0010977	negative regulation of neuron projection development
Biological Process	GO:1902999	negative regulation of phospholipid efflux
Biological Process	GO:0010544	negative regulation of platelet activation
Biological Process	GO:1901627	negative regulation of postsynaptic membrane organization
Biological Process	GO:0051248	negative regulation of protein metabolic process
Biological Process	GO:0050709	negative regulation of protein secretion
Biological Process	GO:0048662	negative regulation of smooth muscle cell proliferation
Biological Process	GO:0090209	negative regulation of triglyceride metabolic process
Biological Process	GO:0031175	neuron projection development
Biological Process	GO:0007263	nitric oxide mediated signal transduction
Biological Process	GO:0033700	phospholipid efflux
Biological Process	GO:0044794	positive regulation by host of viral process
Biological Process	GO:1905920	positive regulation of CoA-transferase activity
Biological Process	GO:0045893	positive regulation of DNA-templated transcription
Biological Process	GO:0070374	positive regulation of ERK1 and ERK2 cascade
Biological Process	GO:1905908	positive regulation of amyloid fibril formation
Biological Process	GO:1900223	positive regulation of amyloid-beta clearance
Biological Process	GO:1902004	positive regulation of amyloid-beta formation
Biological Process	GO:0010875	positive regulation of cholesterol efflux
Biological Process	GO:0090205	positive regulation of cholesterol metabolic process
Biological Process	GO:0060999	positive regulation of dendritic spine development
Biological Process	GO:1902952	positive regulation of dendritic spine maintenance
Biological Process	GO:0045807	positive regulation of endocytosis
Biological Process	GO:1905855	positive regulation of heparan sulfate binding
Biological Process	GO:1905860	positive regulation of heparan sulfate proteoglycan binding
Biological Process	GO:0046889	positive regulation of lipid biosynthetic process
Biological Process	GO:1903002	positive regulation of lipid transport across blood-brain barrier
Biological Process	GO:0032805	positive regulation of low-density lipoprotein particle receptor catabolic process
Biological Process	GO:0051044	positive regulation of membrane protein ectodomain proteolysis
Biological Process	GO:1902998	positive regulation of neurofibrillary tangle assembly
Biological Process	GO:1901216	positive regulation of neuron death
Biological Process	GO:0010976	positive regulation of neuron projection development
Biological Process	GO:0051000	positive regulation of nitric-oxide synthase activity
Biological Process	GO:1902995	positive regulation of phospholipid efflux
Biological Process	GO:1901631	positive regulation of presynaptic membrane organization
Biological Process	GO:0017038	protein import
Biological Process	GO:0006898	receptor-mediated endocytosis
Biological Process	GO:0032489	regulation of Cdc42 protein signal transduction
Biological Process	GO:1905906	regulation of amyloid fibril formation
Biological Process	GO:1902991	regulation of amyloid precursor protein catabolic process
Biological Process	GO:1900221	regulation of amyloid-beta clearance
Biological Process	GO:0030516	regulation of axon extension
Biological Process	GO:2000822	regulation of behavioral fear response
Biological Process	GO:1905890	regulation of cellular response to very-low-density lipoprotein particle stimulus
Biological Process	GO:0090181	regulation of cholesterol metabolic process
Biological Process	GO:0045088	regulation of innate immune response
Biological Process	GO:1901214	regulation of neuron death
Biological Process	GO:0048168	regulation of neuronal synaptic plasticity
Biological Process	GO:0061136	regulation of proteasomal protein catabolic process
Biological Process	GO:0051246	regulation of protein metabolic process
Biological Process	GO:0043254	regulation of protein-containing complex assembly
Biological Process	GO:1902947	regulation of tau-protein kinase activity
Biological Process	GO:0061771	response to caloric restriction
Biological Process	GO:0002021	response to dietary excess
Biological Process	GO:0000302	response to reactive oxygen species
Biological Process	GO:0043691	reverse cholesterol transport
Biological Process	GO:0007271	synaptic transmission, cholinergic
Biological Process	GO:0070328	triglyceride homeostasis
Biological Process	GO:0006641	triglyceride metabolic process
Biological Process	GO:0071830	triglyceride-rich lipoprotein particle clearance
Biological Process	GO:0042311	vasodilation
Biological Process	GO:0034447	very-low-density lipoprotein particle clearance
Biological Process	GO:0034372	very-low-density lipoprotein particle remodeling
Biological Process	GO:0019068	virion assembly
Molecular Function	GO:0001540	amyloid-beta binding
Molecular Function	GO:0016209	antioxidant activity
Molecular Function	GO:0120020	cholesterol transfer activity
Molecular Function	GO:0019899	enzyme binding
Molecular Function	GO:0043395	heparan sulfate proteoglycan binding
Molecular Function	GO:0008201	heparin binding
Molecular Function	GO:0042802	identical protein binding
Molecular Function	GO:0008289	lipid binding
Molecular Function	GO:0005319	lipid transporter activity
Molecular Function	GO:0071813	lipoprotein particle binding
Molecular Function	GO:0050750	low-density lipoprotein particle receptor binding
Molecular Function	GO:0046911	metal chelating activity
Molecular Function	GO:0060228	phosphatidylcholine-sterol O-acyltransferase activator activity
Molecular Function	GO:0005543	phospholipid binding
Molecular Function	GO:0046983	protein dimerization activity
Molecular Function	GO:0042803	protein homodimerization activity
Molecular Function	GO:0044877	protein-containing complex binding
Molecular Function	GO:0005102	signaling receptor binding
Molecular Function	GO:0005198	structural molecule activity
Molecular Function	GO:0048156	tau protein binding
Molecular Function	GO:0070326	very-low-density lipoprotein particle receptor binding
Cellular Component	GO:0005794	Golgi apparatus
Cellular Component	GO:0072562	blood microparticle
Cellular Component	GO:0042627	chylomicron
Cellular Component	GO:0030669	clathrin-coated endocytic vesicle membrane
Cellular Component	GO:0062023	collagen-containing extracellular matrix
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0030425	dendrite
Cellular Component	GO:0034365	discoidal high-density lipoprotein particle
Cellular Component	GO:0005769	early endosome
Cellular Component	GO:0071682	endocytic vesicle lumen
Cellular Component	GO:0005783	endoplasmic reticulum
Cellular Component	GO:0005788	endoplasmic reticulum lumen
Cellular Component	GO:0070062	extracellular exosome
Cellular Component	GO:0031012	extracellular matrix
Cellular Component	GO:0005576	extracellular region
Cellular Component	GO:0005615	extracellular space
Cellular Component	GO:1903561	extracellular vesicle
Cellular Component	GO:0098978	glutamatergic synapse
Cellular Component	GO:0034364	high-density lipoprotein particle
Cellular Component	GO:0034363	intermediate-density lipoprotein particle
Cellular Component	GO:1990777	lipoprotein particle
Cellular Component	GO:0034362	low-density lipoprotein particle
Cellular Component	GO:0042470	melanosome
Cellular Component	GO:0016020	membrane
Cellular Component	GO:0097487	multivesicular body, internal vesicle
Cellular Component	GO:0043025	neuronal cell body
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0005886	plasma membrane
Cellular Component	GO:0043083	synaptic cleft
Cellular Component	GO:0034361	very-low-density lipoprotein particle

InterPro / Pfam

InterPro	InterPro name
IPR000074	Apolipoprotein A/E

Pfam	Pfam name
PF01442	Apolipoprotein A1/A4/E domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1251985	Nuclear signaling by ERBB4	Leaf	R-HSA-162582	Signal Transduction
R-HSA-3000480	Scavenging by Class A Receptors	Leaf	R-HSA-5653656	Vesicle-mediated transport
R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-8864260	Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-8957275	Post-translational protein phosphorylation	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-8963888	Chylomicron assembly	Leaf	R-HSA-382551	Transport of small molecules
R-HSA-8963901	Chylomicron remodeling	Leaf	R-HSA-382551	Transport of small molecules
R-HSA-8964026	Chylomicron clearance	Leaf	R-HSA-382551	Transport of small molecules
R-HSA-8964058	HDL remodeling	Leaf	R-HSA-382551	Transport of small molecules
R-HSA-9029569	NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux	Leaf	R-HSA-162582	Signal Transduction
R-HSA-975634	Retinoid metabolism and transport	Leaf	R-HSA-9709957	Sensory Perception
R-HSA-977225	Amyloid fiber formation	Leaf	R-HSA-392499	Metabolism of proteins

Subcellular location

Location	ECO term	Pubmed
Endosome, multivesicular body	ECO:0000269	PubMed:26387950
Extracellular vesicle	ECO:0000269	PubMed:26387950
Secreted	ECO:0000269	PubMed:2498325
Secreted	ECO:0000269	PubMed:30333625
Secreted, extracellular space	ECO:0000269	PubMed:8340399
Secreted, extracellular space, extracellular matrix	ECO:0000269	PubMed:9488694

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000006	Autosomal dominant inheritance
HP:0000007	Autosomal recessive inheritance
HP:0000083	Renal insufficiency
HP:0000093	Proteinuria
HP:0000488	Retinopathy
HP:0000498	Blepharitis
HP:0000529	Progressive visual loss
HP:0000608	Macular degeneration
HP:0000726	Dementia
HP:0000751	Personality changes
HP:0000799	Renal steatosis
HP:0000819	Diabetes mellitus
HP:0000821	Hypothyroidism
HP:0000951	Abnormality of the skin
HP:0000953	Hyperpigmentation of the skin
HP:0000967	Petechiae
HP:0000969	Edema
HP:0001010	Hypopigmentation of the skin
HP:0001084	Corneal arcus
HP:0001114	Xanthelasma
HP:0001250	Seizure
HP:0001260	Dysarthria
HP:0001285	Spastic tetraparesis
HP:0001288	Gait disturbance
HP:0001300	Parkinsonism
HP:0001332	Dystonia
HP:0001336	Myoclonus
HP:0001394	Cirrhosis
HP:0001397	Hepatic steatosis
HP:0001482	Subcutaneous nodule
HP:0001513	Obesity
HP:0001681	Angina pectoris
HP:0001735	Acute pancreatitis
HP:0001744	Splenomegaly
HP:0001873	Thrombocytopenia
HP:0001892	Abnormal bleeding
HP:0001982	Sea-blue histiocytosis
HP:0001997	Gout
HP:0002015	Dysphagia
HP:0002071	Abnormality of extrapyramidal motor function
HP:0002113	Pulmonary infiltrates
HP:0002120	Cerebral cortical atrophy
HP:0002155	Hypertriglyceridemia
HP:0002185	Neurofibrillary tangles
HP:0002186	Apraxia
HP:0002221	Absent axillary hair
HP:0002240	Hepatomegaly
HP:0002354	Memory impairment
HP:0002395	Lower limb hyperreflexia
HP:0002423	Long-tract signs
HP:0002511	Alzheimer disease
HP:0002635	Type IV atherosclerotic lesion
HP:0003124	Hypercholesterolemia
HP:0003141	Increased LDL cholesterol concentration
HP:0003233	Decreased HDL cholesterol concentration
HP:0003487	Babinski sign
HP:0003581	Adult onset
HP:0003584	Late onset
HP:0003596	Middle age onset
HP:0003651	Foam cells
HP:0003678	Rapidly progressive
HP:0004943	Accelerated atherosclerosis
HP:0004950	Peripheral arterial stenosis
HP:0005181	Premature coronary artery atherosclerosis
HP:0006979	Sleep-wake cycle disturbance
HP:0010524	Agnosia
HP:0010874	Tendon xanthomatosis
HP:0011506	Choroidal neovascularization
HP:0011970	Cerebral amyloid angiopathy
HP:0012397	Aortic atherosclerotic lesion
HP:0012574	Mesangial hypercellularity
HP:0012643	Foveal hypopigmentation
HP:0012662	Parietal hypometabolism in FDG PET
HP:0025574	Macular hemorrhage
HP:0030499	Macular drusen
HP:0031609	Geographic atrophy
HP:0031868	Optic ataxia
HP:0031956	Elevated circulating aspartate aminotransferase concentration
HP:0031964	Elevated circulating alanine aminotransferase concentration
HP:0100256	Senile plaques
HP:0100543	Cognitive impairment
HP:0100721	Mediastinal lymphadenopathy
HP:0100820	Glomerulopathy

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	High	Enhanced
bone marrow	hematopoietic cells	Low	Enhanced
caudate	glial cells	High	Enhanced
caudate	neuronal cells	High	Enhanced
cerebellum	Bergmann glia - cytoplasm/membrane	Medium	Enhanced
cerebellum	Purkinje cells - cytoplasm/membrane	Low	Enhanced
cerebellum	granular cells - cytoplasm/membrane	Medium	Enhanced
cerebellum	granular cells - nucleus	Medium	Enhanced
cerebellum	molecular layer - neuropil	Low	Enhanced
cerebellum	molecular layer cells - cytoplasm/membrane	High	Enhanced
cerebellum	processes in molecular layer	Medium	Enhanced
cerebellum	synaptic glomeruli - capsule	Low	Enhanced
cerebellum	white matter cells - cytoplasm/membrane	Medium	Enhanced
cerebellum	white matter cells - nucleus	Medium	Enhanced
cerebral cortex	endothelial cells	Medium	Enhanced
cerebral cortex	glial cells	High	Enhanced
cerebral cortex	neuronal cells	High	Enhanced
cerebral cortex	neuropil	Low	Enhanced
endometrium	ciliated epithelial cells	High	Enhanced
endometrium	nonciliated glandular epithelial cells	Medium	Enhanced
endometrium	nonciliated luminal epithelial cells	High	Enhanced
endometrium	smooth muscle cells	Medium	Enhanced
hippocampus	glial cells	Medium	Enhanced
hippocampus	neuronal cells	High	Enhanced
kidney	proximal tubules (cell body)	Medium	Enhanced
liver	hepatocytes	Medium	Enhanced
placenta	decidual cells	Medium	Enhanced
placenta	endothelial cells	High	Enhanced
placenta	hofbauer cells	High	Enhanced
skin 1	cells in granular layer	Low	Enhanced
skin 1	cells in spinous layer	Medium	Enhanced
skin 1	extracellular matrix	High	Enhanced
skin 1	fibrohistiocytic cells	High	Enhanced
skin 1	hair follicles	High	Enhanced
skin 1	sebaceous glands	High	Enhanced
skin 2	cells in spinous layer	Low	Enhanced
skin 2	endothelial cells	Medium	Enhanced
skin 2	extracellular matrix	Low	Enhanced
testis	Leydig cells	Low	Enhanced

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
alzheimer disease 2	MONDO:0007089	G30	chapter6, Diseases of the nervous system	OMIM:104310
sea-blue histiocyte syndrome	MONDO:0010017	D76	chapter3, Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism	OMIM:269600	Orphanet:158029
lipoprotein glomerulopathy	MONDO:0012725	N07	chapter14, Diseases of the genitourinary system	OMIM:611771	Orphanet:329481
hyperlipoproteinemia type 3	MONDO:0018473	E78	chapter4, Endocrine, nutritional and metabolic diseases	OMIM:617347	Orphanet:412

Summary of P02649

Gene: APOE
Protein: Apolipoprotein E

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P02649

Gene: APOE Protein: Apolipoprotein E

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: APOE
Protein: Apolipoprotein E