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- PDB-2l7b: NMR Structure of full length apoE3 -

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Basic information

Entry
Database: PDB / ID: 2l7b
TitleNMR Structure of full length apoE3
ComponentsApolipoprotein E
KeywordsLIPID TRANSPORT / apolipoprotein E / Atherosclerosis / Alzheimer's Disease
Function / homology
Function and homology information


lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process ...lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / positive regulation of lipoprotein transport / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / Chylomicron remodeling / lipid transporter activity / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of amyloid fibril formation / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / regulation of protein metabolic process / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / AMPA glutamate receptor clustering / lipoprotein catabolic process / melanosome organization / multivesicular body, internal vesicle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / Scavenging by Class A Receptors / triglyceride metabolic process / positive regulation of dendritic spine development / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / negative regulation of blood vessel endothelial cell migration / regulation of neuronal synaptic plasticity / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of dendritic spine maintenance / negative regulation of blood coagulation / positive regulation of cholesterol efflux / negative regulation of MAP kinase activity / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailslowest energy, model 1
AuthorsChen, J. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Topology of human apolipoprotein E3 uniquely regulates its diverse biological functions.
Authors: Chen, J. / Li, Q. / Wang, J.
History
DepositionDec 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein E


Theoretical massNumber of molelcules
Total (without water)35,3021
Polymers35,3021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 35301.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Production host: Escherichia coli (E. coli) / References: UniProt: P02649

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of full length apoE3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1623D 1H-15N NOESY
1724D CN NOESY
1823D (H)CCH-TOCSY
1923D CCC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] apoE3, 100 mM sodium phosphate, 10 mM DTT, 5 mM [U-100% 2H] EDTA, 1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N; U-50% 2H] apoE3, 10 mM DTT, 1 mM DSS, 5 mM [U-100% 2H] EDTA, 100 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMapoE3-1[U-13C; U-15N; U-2H]1
100 mMsodium phosphate-21
10 mMDTT-31
5 mMEDTA-4[U-100% 2H]1
1 mMDSS-51
1 mMapoE3-6[U-100% 13C; U-100% 15N; U-50% 2H]2
10 mMDTT-72
1 mMDSS-82
5 mMEDTA-9[U-100% 2H]2
100 mMsodium phosphate-102
Sample conditionsIonic strength: 0.1 / pH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
PIPPGarrettchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
ProcheckNMRLaskowski and MacArthurgeometry optimization
ProcheckNMRLaskowski and MacArthurrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 204 / Protein psi angle constraints total count: 204
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.311 °
Conformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.4 ° / Maximum upper distance constraint violation: 0.58 Å / Torsion angle constraint violation method: CYANA
NMR ensemble rmsDistance rms dev: 0.0124 Å / Distance rms dev error: 0.0012 Å

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