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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


chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle / regulation of amyloid-beta clearance / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle remodeling / Chylomicron clearance / negative regulation of triglyceride metabolic process / response to caloric restriction / acylglycerol homeostasis / NMDA glutamate receptor clustering / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / regulation of amyloid fibril formation / regulation of protein metabolic process / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / melanosome organization / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / positive regulation by host of viral process / very-low-density lipoprotein particle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / cholesterol transfer activity / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / protein import / negative regulation of blood coagulation / high-density lipoprotein particle / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / synaptic transmission, cholinergic / heparan sulfate proteoglycan binding / negative regulation of cholesterol biosynthetic process / amyloid precursor protein metabolic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / negative regulation of protein metabolic process / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding / triglyceride metabolic process / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / locomotory exploration behavior / regulation of neuronal synaptic plasticity / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / lipoprotein particle binding / positive regulation of endocytosis / antioxidant activity / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / positive regulation of cholesterol efflux / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / synaptic cleft / regulation of proteasomal protein catabolic process
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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