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- PDB-1ya9: Crystal Structure of the 22kDa N-Terminal Fragment of Mouse Apoli... -

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Basic information

Entry
Database: PDB / ID: 1ya9
TitleCrystal Structure of the 22kDa N-Terminal Fragment of Mouse Apolipoprotein E
ComponentsApolipoprotein E
KeywordsLIPID TRANSPORT / Apolipoprotein E / LDL receptor binding
Function / homology
Function and homology information


regulation of plasma lipoprotein particle levels / Chylomicron clearance / Chylomicron assembly / Chylomicron remodeling / HDL remodeling / Scavenging by Class A Receptors / Retinoid metabolism and transport / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / lipid transport involved in lipid storage ...regulation of plasma lipoprotein particle levels / Chylomicron clearance / Chylomicron assembly / Chylomicron remodeling / HDL remodeling / Scavenging by Class A Receptors / Retinoid metabolism and transport / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / lipid transport involved in lipid storage / 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 / negative regulation of cholesterol biosynthetic process / positive regulation of lipoprotein transport / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle remodeling / circulatory system development / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / artery development / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / : / lipoprotein metabolic process / high-density lipoprotein particle clearance / phospholipid efflux / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / lipoprotein catabolic process / melanosome organization / multivesicular body, internal vesicle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / positive regulation of membrane protein ectodomain proteolysis / cholesterol efflux / artery morphogenesis / triglyceride metabolic process / positive regulation of dendritic spine development / low-density lipoprotein particle receptor binding / regulation of innate immune response / virion assembly / regulation of synapse organization / lipid homeostasis / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of dendritic spine maintenance / positive regulation of cholesterol efflux / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / nitric oxide-cGMP-mediated signaling / regulation of proteasomal protein catabolic process / extracellular matrix / receptor-mediated endocytosis / cholesterol metabolic process / cholesterol homeostasis / negative regulation of smooth muscle cell proliferation / negative regulation of canonical Wnt signaling pathway / positive regulation of neuron projection development / phospholipid binding / tau protein binding / lipid metabolic process / negative regulation of inflammatory response
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPeters-Libeu, C.A. / Rutenber, E. / Newhouse, Y. / Hatters, D.M. / Weisgraber, K.H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Engineering conformational destabilization into mouse apolipoprotein E. A model for a unique property of human apolipoprotein E4
Authors: Hatters, D.M. / Peters-Libeu, C.A. / Weisgraber, K.H.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,0531
Polymers21,0531
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.034, 49.233, 112.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 21052.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoe / Production host: Escherichia coli (E. coli)
Keywords: 22kDa N-Terminal Fragment of Mouse Apolipoprotein E, (residue 20-200, SWS)
References: UniProt: P08226
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.4 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.09→20 Å / Num. all: 10097 / Num. obs: 9944 / Biso Wilson estimate: 14.1 Å2
Reflection shellResolution: 2.09→2.13 Å / % possible all: 87

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
EPMRphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→18.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0.01 / SU B: 6.261 / SU ML: 0.171 / Data cutoff high absF: 1263371.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 512 5.1 %RANDOM
Rwork0.215 ---
obs0.215 9944 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1753 Å2 / ksol: 0.352492 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---2.75 Å20 Å2
3---4.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.09→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 83 1448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.09→2.13 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 20 4.9 %
Rwork0.229 391 -
obs--22 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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