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- PDB-2kc3: NMR solution structure of complete receptor binding domain of hum... -

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Basic information

Entry
Database: PDB / ID: 2kc3
TitleNMR solution structure of complete receptor binding domain of human apolipoprotein E
ComponentsApolipoprotein E
KeywordsLIPOPROTEIN / ApoE / LDLR / VLDLR / Receptor binding domain / Lipid transport / Alzheimer disease / Chylomicron / Disease mutation / Glycation / Glycoprotein / HDL / Heparin-binding / Hyperlipidemia / Polymorphism / Secreted / Transport / VLDL
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 / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsApoE N-terminal domain (BMRB title). Contains structural features (buried hydrophilic residues and ...ApoE N-terminal domain (BMRB title). Contains structural features (buried hydrophilic residues and H-bonds) that are present in at least 10 of the 20 conformers, model 1
AuthorsWang, J. / Sivashanmugam, A.
CitationJournal: To be Published
Title: A complete receptor binding domain of human apolipoprotein E
Authors: Sivashanmugam, A. / Wang, J.
History
DepositionDec 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Apolipoprotein E


Theoretical massNumber of molelcules
Total (without water)21,3531
Polymers21,3531
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 / 100structures with the lowest energy and least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 21353.176 Da / Num. of mol.: 1 / Fragment: UNP residues 19-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02649

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HN(CO)CA
1413D HN(COCA)CB
1513D HNCA
1623D 1H-15N NOESY
1723D C(CO)NH
1823D H(CCO)NH
1923D (H)CCH-TOCSY
11024D 15N-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N; U-70% 2H] Human apolipoprotein E N-terminal domain-1, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N; U-30% 2H] Human apolipoprotein E N-terminal domain-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHuman apolipoprotein E N-terminal domain-1[U-100% 13C; U-100% 15N; U-70% 2H]1
1 mMHuman apolipoprotein E N-terminal domain-2[U-100% 13C; U-100% 15N; U-30% 2H]2
Sample conditionsIonic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
ProcheckNMRLaskowski and MacArthurdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2980 / Hydrogen bond constraints total count: 218
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy and least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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