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- PDB-2n5e: The 3D solution structure of discoidal high-density lipoprotein p... -

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Basic information

Entry
Database: PDB / ID: 2n5e
TitleThe 3D solution structure of discoidal high-density lipoprotein particles
ComponentsApolipoprotein A-I
KeywordsLIPID BINDING PROTEIN / nanodisc / HDL / lipoproteins / cardiovascular disease
Function / homology
Function and homology information


Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport ...Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / ABC transporters in lipid homeostasis / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle clearance / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / very-low-density lipoprotein particle / reverse cholesterol transport / cholesterol transfer activity / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / negative chemotaxis / adrenal gland development / positive regulation of Rho protein signal transduction / cholesterol binding / cholesterol biosynthetic process / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / Scavenging of heme from plasma / Retinoid metabolism and transport / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / cholesterol metabolic process / integrin-mediated signaling pathway / cholesterol homeostasis / Post-translational protein phosphorylation / regulation of protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / Platelet degranulation / amyloid-beta binding / cytoplasmic vesicle / secretory granule lumen / collagen-containing extracellular matrix / early endosome / protein stabilization / blood microparticle / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Apolipoprotein A/E / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBibow, S. / Polyhach, Y. / Eichmann, C. / Chi, C.N. / Kowal, J. / Stahlberg, H. / Jeschke, G. / Guentert, P. / Riek, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2017
Title: Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I.
Authors: Bibow, S. / Polyhach, Y. / Eichmann, C. / Chi, C.N. / Kowal, J. / Albiez, S. / McLeod, R.A. / Stahlberg, H. / Jeschke, G. / Guntert, P. / Riek, R.
History
DepositionJul 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein A-I
B: Apolipoprotein A-I


Theoretical massNumber of molelcules
Total (without water)38,9242
Polymers38,9242
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)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A1 / Proapolipoprotein A-I / ProapoA-I / Truncated apolipoprotein ...Apo-AI / ApoA-I / Apolipoprotein A1 / Proapolipoprotein A-I / ProapoA-I / Truncated apolipoprotein A-I / Apolipoprotein A-I(1-242)


Mass: 19461.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02647

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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 HNCO
1313D HNCA
1413D HN(CA)CB
1513D 1H-15N NOESY
1612D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5-1.0 mM [U-99% 13C; U-99% 15N] H2O, 1 mM stereospecific Methyl-labeling H2O, 1 mM selective unlabeling H2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMH2O-1[U-99% 13C; U-99% 15N]0.5-1.01
1 mMH2O-2stereospecific Methyl-labeling1
1 mMH2O-3selective unlabeling1
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: ambient / Temperature: 316 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
CYANA3.97Guntert, Braun and Wuthrichstructure solution
CYANA3.97Guntert, Braun and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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