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- PDB-1or3: APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165 -

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Basic information

Entry
Database: PDB / ID: 1or3
TitleAPOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165
ComponentsPROTEIN (APOLIPOPROTEIN E)
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA PROTEIN / HDL / VLDL
Function / homology
Function and homology information


lipid transport involved in lipid storage / maintenance of location in cell / 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 / discoidal high-density lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors ...lipid transport involved in lipid storage / maintenance of location in cell / 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 / discoidal high-density lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / negative regulation of cholesterol biosynthetic process / chylomicron remnant / lipoprotein particle / regulation of amyloid-beta clearance / intermediate-density lipoprotein particle / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / Chylomicron clearance / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipid carrier activity / positive regulation of low-density lipoprotein particle receptor catabolic process / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / very-low-density lipoprotein particle clearance / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / chylomicron / high-density lipoprotein particle remodeling / multivesicular body, internal vesicle / positive regulation of amyloid-beta clearance / reverse cholesterol transport / positive regulation of cholesterol metabolic process / regulation of amyloid fibril formation / high-density lipoprotein particle assembly / host-mediated activation of viral process / lipoprotein biosynthetic process / melanosome organization / cholesterol transfer activity / regulation of behavioral fear response / low-density lipoprotein particle / cholesterol catabolic process / protein import / high-density lipoprotein particle / very-low-density lipoprotein particle / low-density lipoprotein particle remodeling / amyloid precursor protein metabolic process / response to caloric restriction / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of endothelial cell migration / HDL remodeling / negative regulation of protein metabolic process / artery morphogenesis / cholesterol efflux / regulation of cholesterol metabolic process / regulation of axon extension / synaptic transmission, cholinergic / Scavenging by Class A Receptors / triglyceride metabolic process / triglyceride homeostasis / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / virion assembly / regulation of innate immune response / negative regulation of endothelial cell proliferation / negative regulation of platelet-derived growth factor receptor signaling pathway / antioxidant activity / positive regulation of lipoprotein transport / response to dietary excess / positive regulation of dendritic spine development / negative regulation of amyloid-beta formation / lipoprotein particle binding / AMPA glutamate receptor clustering / negative regulation of blood vessel endothelial cell migration / negative regulation of platelet activation / negative regulation of long-term synaptic potentiation / locomotory exploration behavior / negative regulation of blood coagulation / negative regulation of protein secretion / positive regulation of cholesterol efflux / positive regulation of dendritic spine maintenance / fatty acid homeostasis / intracellular transport / regulation of protein-containing complex assembly / positive regulation of endocytosis / regulation of neuronal synaptic plasticity / long-chain fatty acid transport / Nuclear signaling by ERBB4 / positive regulation of lipid biosynthetic process / cholesterol metabolic 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 / MAD / Resolution: 1.73 Å
AuthorsRupp, B. / Segelke, B.W.
CitationJournal: Protein Sci. / Year: 2000
Title: Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding.
Authors: Segelke, B.W. / Forstner, M. / Knapp, M. / Trakhanov, S.D. / Parkin, S. / Newhouse, Y.M. / Bellamy, H.D. / Weisgraber, K.H. / Rupp, B.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (APOLIPOPROTEIN E)


Theoretical massNumber of molelcules
Total (without water)19,2981
Polymers19,2981
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.370, 47.370, 104.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-114-

ARG

21A-212-

HOH

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Components

#1: Protein PROTEIN (APOLIPOPROTEIN E) / APOE3


Mass: 19297.805 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE MUTANT USED IN MAD PHASING EXPERIMENT
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21, B834(DE)MET- / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, B834(DE)MET- / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.76 Å3/Da / Density % sol: 30 %
Description: 4 WAVELENGTHS USED FOR PHASING (ALS BEAMLINE 5.0.2)
Crystal growpH: 5.6
Details: RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2).
Components of the solutions
IDNameCrystal-IDSol-ID
150MM NA-Cacodylate, pH 5.612
210-20% PEG 40012
31% 2-ME12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 %PEG4001reservoir
250 mMsodium cacodylate1reservoir
320 mM1dropNH4HCO3
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: May 15, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→25 Å / Num. obs: 16782 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 27.4
Reflection shellResolution: 1.73→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.7 / Rsym value: 22.5 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 48854
Reflection shell
*PLUS
% possible obs: 89.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLORmodel building
CCP4model building
X-PLOR3.851refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.73→10 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.238 1339 10.1 %RANDOM
Rwork0.229 ---
obs-13222 89.9 %-
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-3.35 Å20 Å2
2---1.23 Å20 Å2
3---2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-8 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.73→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 158 1306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.291.5
X-RAY DIFFRACTIONx_mcangle_it6.622
X-RAY DIFFRACTIONx_scbond_it7.232
X-RAY DIFFRACTIONx_scangle_it11.12.5
LS refinement shellResolution: 1.73→1.79 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 967 10.4 %
Rwork0.33 112 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PATOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETE
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.33

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