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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 / maintenance of location in cell / 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 / negative regulation of triglyceride metabolic process / discoidal high-density lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors ...lipid transport involved in lipid storage / maintenance of location in cell / 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 / negative regulation of triglyceride metabolic process / discoidal high-density lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / negative regulation of cholesterol biosynthetic process / chylomicron remnant / lipoprotein particle / regulation of amyloid-beta clearance / intermediate-density lipoprotein particle / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / Chylomicron clearance / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipid carrier activity / positive regulation of low-density lipoprotein particle receptor catabolic process / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / very-low-density lipoprotein particle clearance / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / chylomicron / high-density lipoprotein particle remodeling / multivesicular body, internal vesicle / positive regulation of amyloid-beta clearance / reverse cholesterol transport / positive regulation of cholesterol metabolic process / regulation of amyloid fibril formation / high-density lipoprotein particle assembly / host-mediated activation of viral process / lipoprotein biosynthetic process / melanosome organization / cholesterol transfer activity / regulation of behavioral fear response / low-density lipoprotein particle / cholesterol catabolic process / protein import / high-density lipoprotein particle / very-low-density lipoprotein particle / low-density lipoprotein particle remodeling / amyloid precursor protein metabolic process / response to caloric restriction / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / regulation of Cdc42 protein signal transduction / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of endothelial cell migration / HDL remodeling / artery morphogenesis / negative regulation of protein metabolic process / cholesterol efflux / regulation of cholesterol metabolic process / regulation of axon extension / Scavenging by Class A Receptors / triglyceride metabolic process / triglyceride homeostasis / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / virion assembly / regulation of innate immune response / negative regulation of endothelial cell proliferation / negative regulation of platelet-derived growth factor receptor signaling pathway / antioxidant activity / positive regulation of lipoprotein transport / response to dietary excess / positive regulation of dendritic spine development / negative regulation of amyloid-beta formation / lipoprotein particle binding / AMPA glutamate receptor clustering / negative regulation of long-term synaptic potentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of platelet activation / locomotory exploration behavior / negative regulation of blood coagulation / negative regulation of protein secretion / positive regulation of cholesterol efflux / positive regulation of dendritic spine maintenance / fatty acid homeostasis / intracellular transport / regulation of protein-containing complex assembly / positive regulation of endocytosis / regulation of neuronal synaptic plasticity / long-chain fatty acid transport / Nuclear signaling by ERBB4 / positive regulation of lipid biosynthetic process / cholesterol metabolic 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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