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- PDB-3k2s: Solution structure of double super helix model -

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Basic information

Entry
Database: PDB / ID: 3k2s
TitleSolution structure of double super helix model
ComponentsApolipoprotein A-IApolipoprotein AI
KeywordsLIPID BINDING PROTEIN / super double helix / amphipathic / Amyloid / Amyloidosis / Atherosclerosis / Cholesterol metabolism / Disease mutation / Glycation / Glycoprotein / HDL / Lipid metabolism / Lipid transport / Lipoprotein / Neuropathy / Palmitate / Secreted / Steroid metabolism / Transport / HIGH DENSITY LIPOPROTEIN
Function / homology
Function and homology information


high-density lipoprotein particle receptor binding / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / regulation of intestinal cholesterol absorption / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport ...high-density lipoprotein particle receptor binding / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / regulation of intestinal cholesterol absorption / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / positive regulation of phospholipid efflux / high-density lipoprotein particle binding / cholesterol import / Chylomicron assembly / positive regulation of cholesterol metabolic process / negative regulation of heterotypic cell-cell adhesion / high-density lipoprotein particle remodeling / blood vessel endothelial cell migration / ABC transporters in lipid homeostasis / phospholipid efflux / apolipoprotein receptor binding / high-density lipoprotein particle clearance / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / apolipoprotein A-I receptor binding / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / cholesterol transfer activity / reverse cholesterol transport / phosphatidylcholine biosynthetic process / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / lipoprotein biosynthetic process / glucocorticoid metabolic process / positive regulation of CoA-transferase activity / phosphatidylcholine metabolic process / lipid storage / phospholipid homeostasis / high-density lipoprotein particle / triglyceride homeostasis / regulation of Cdc42 protein signal transduction / cholesterol transport / chemorepellent activity / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / endothelial cell proliferation / cholesterol binding / negative regulation of interleukin-1 beta production / positive regulation of Rho protein signal transduction / negative chemotaxis / adrenal gland development / cholesterol biosynthetic process / positive regulation of cholesterol efflux / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / Retinoid metabolism and transport / Scavenging of heme from plasma / positive regulation of phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / endocytic vesicle lumen / positive regulation of stress fiber assembly / cholesterol metabolic process / heat shock protein binding / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / phospholipid binding / regulation of protein phosphorylation / Heme signaling / PPARA activates gene expression / 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 / collagen-containing extracellular matrix / blood microparticle / secretory granule lumen / protein stabilization / early endosome / 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
CHOLESTEROL / Chem-POV / Apolipoprotein A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / NUCLEAR REACTOR
AuthorsWu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.-M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. ...Wu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.-M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. / Gutsche, I. / Zaccai, G. / Didonato, J.A. / Hazen, L.S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Double superhelix model of high density lipoprotein.
Authors: Wu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. / Gutsche, I. / Zaccai, G. / Didonato, J.A. / Hazen, S.L.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,990222
Polymers56,2412
Non-polymers159,748220
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Apolipoprotein A-I / Apolipoprotein AI / Apo-AI / ApoA-I / Apolipoprotein A-I(1-242)


Mass: 28120.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 200 / Source method: obtained synthetically / Formula: C42H82NO8P / Details: POPC / Comment: phospholipid*YM
#3: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C27H46O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING / Number of used crystals: 1

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: NUCLEAR REACTOR / Type: OTHER / Wavelength: 5 Å
DetectorDetector: AREA DETECTOR / Date: Oct 15, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 5 Å / Relative weight: 1
Reflection shellHighest resolution: 5 Å
Soln scatter

Conc. range: 2-4 / Data analysis software list: PRIMUS, GNOM, DAMMIN / Data reduction software list: ILL IN-HOUSE PACKAGE / Detector type: AREA / Num. of time frames: 3 / Sample pH: 7.4 / Source beamline: NEUTRON CAMERA FOR REACTOR SOURCE / Source beamline instrument: D22 (LOQ) / Source class: N / Source type: ILL / Temperature: 301 K / Type: neutron

IDBuffer nameMean guiner radius (nm)Mean guiner radius esd (nm)Protein length
1PBS IN 12% D2O5.130.0417.3
2PBS IN 42% D2O3.970.0515.2

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Processing

Software
NameVersionClassification
ILLsoftwaredata collection
PRIMUSmodel building
GNOMmodel building
DAMMINmodel building
GROMACSrefinement
SASSIMrefinement
DEXANALrefinement
ILLsoftwaredata reduction
ILLsoftwaredata scaling
PRIMUSphasing
GNOMphasing
DAMMINphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 10960 0 14920
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT CHI SQUARE-FACTOR DEFINED BY THE DIFFERENCE BETWEEN THE CALCULATED AND EXPERIMENTAL SCATTERING INTENSITIES AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 2.4 NM-1 (PROTEIN) AND 2.1 NM-1 (LIPID).
Details: AN ALL ATOM COMPUTATIONAL MODEL WAS CONSTRUCTED BY COMBINING MOLELING WITH CONRAST VARIATION SANS, HYDROGEN-DEUTERIUM EXCHANGE (H/D-MS/MS), AND DISTANCE CONSTRAINTS FROM CROSS-LINKING, ...Details: AN ALL ATOM COMPUTATIONAL MODEL WAS CONSTRUCTED BY COMBINING MOLELING WITH CONRAST VARIATION SANS, HYDROGEN-DEUTERIUM EXCHANGE (H/D-MS/MS), AND DISTANCE CONSTRAINTS FROM CROSS-LINKING, FLUORESCENCE RESONANCE ENERGY TRANSFER AND ELECTRON SPIN RESONANCE. SANS LOW RESOLUTION STRUCTURES (12% AND 42% D2O) WERE USED AS SCAFFOLDS TO BUILD MOLECULAR MODELS FOR PROTEIN AND LIPID COMPONENTS OF NASCENT HDL. 256 MODELS WERE GENERATED AND ASSESSED USING GOODNESS-OF-FIT WITH BOTH SANS AND H/D-MS/MS DATA. THE NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING ALL ATOM STRUCTURE, AND WITH CORRECTIONS FOR WAVELENGTH SPREAD AND BEAM DIVERGENCE.
Entry fitting list: THE DOUBLE BELT MODEL (SEGREST JP, JBC 274, 31755 (1999))
Num. of conformers calculated: 256 / Num. of conformers submitted: 1 / Representative conformer: 1
Software author list: LINDAHL E, SALI A, DELANO WL, MERZEL F, RICHARDS RM, SVERGUN DI
Software list: GROMACS, MODELLER, PYMOL, SASSIM, YALE:VOLUME/ACCESS, PRIMUS, GNOM, DAMMIN

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