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- PDB-1b68: APOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1b68
TitleAPOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT
ComponentsAPOLIPOPROTEIN E
KeywordsLIPID TRANSPORT / HEPARIN-BINDING / PLASMA PROTEIN / HDL / VLDL
Function / homology
Function and homology information


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 / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / maintenance of location in cell ...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 / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / maintenance of location in cell / regulation of amyloid-beta clearance / negative regulation of cholesterol biosynthetic process / positive regulation of lipoprotein transport / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / acylglycerol homeostasis / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / Chylomicron clearance / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of low-density lipoprotein particle receptor catabolic process / response to caloric restriction / cellular response to lipoprotein particle stimulus / very-low-density lipoprotein particle clearance / lipid transporter activity / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / regulation of amyloid fibril formation / lipoprotein catabolic process / AMPA glutamate receptor clustering / high-density lipoprotein particle remodeling / melanosome organization / positive regulation of cholesterol metabolic process / multivesicular body, internal vesicle / regulation of behavioral fear response / reverse cholesterol transport / positive regulation of amyloid-beta clearance / high-density lipoprotein particle assembly / host-mediated activation of viral process / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / protein import / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / heparan sulfate proteoglycan binding / low-density lipoprotein particle remodeling / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / regulation of Cdc42 protein signal transduction / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / regulation of amyloid precursor protein catabolic process / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of cholesterol metabolic process / artery morphogenesis / regulation of axon extension / negative regulation of protein metabolic process / Scavenging by Class A Receptors / triglyceride homeostasis / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / negative regulation of endothelial cell proliferation / positive regulation of dendritic spine development / response to dietary excess / antioxidant activity / negative regulation of MAP kinase activity / negative regulation of amyloid-beta formation / lipoprotein particle binding / locomotory exploration behavior / negative regulation of long-term synaptic potentiation / negative regulation of blood vessel endothelial cell migration / positive regulation of endocytosis / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / positive regulation of cholesterol efflux / negative regulation of protein secretion / fatty acid homeostasis / long-term memory / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport / positive regulation of lipid biosynthetic 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRupp, B. / Peters-Libeu, C.
CitationJournal: Biochemistry / Year: 2001
Title: Interaction of the N-terminal domain of apolipoprotein E4 with heparin.
Authors: Dong, J. / Peters-Libeu, C.A. / Weisgraber, K.H. / Segelke, B.W. / Rupp, B. / Capila, I. / Hernaiz, M.J. / LeBrun, L.A. / Linhardt, R.J.
History
DepositionJan 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)22,2161
Polymers22,2161
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.210, 53.210, 84.760
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 / APOE4


Mass: 22216.135 Da / Num. of mol.: 1
Fragment: 22K FRAGMENT, ISOFORM E4, RECEPTOR BINDING DOMAIN, RESIDUES 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Description: RIGID BODY REFINEMENT ONLY, THEN REBUILD, WARP MAPS USED
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: WELL : 28% PEG 400, 20MM NAOAC, PH 6.0, 0.1% BME PROTEIN SOLN: 40MM (NH4)H(CO3), 7MG/ML PROTEIN DROPS : WELL/PROTEIN 1/3, ROOM TEMPERATURE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %PEG4001reservoir
220 mMsodium acetate1reservoir
30.1 %beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. obs: 16493 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 27.4
Reflection shellResolution: 1.84→1.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.199 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CCP4model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZ4

1bz4


Resolution: 2→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1197 10 %RANDOM
Rwork0.2 ---
obs0.2 11931 94.7 %-
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.68 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-10 Å
Luzzati sigma a0.23 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 133 1305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 183 10 %
Rwork0.298 1650 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.51
LS refinement shell
*PLUS
Rfactor Rfree: 0.321 / Rfactor Rwork: 0.298

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