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- PDB-1or2: APOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165 -

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Basic information

Entry
Database: PDB / ID: 1or2
TitleAPOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165
ComponentsAPOLIPOPROTEIN E
KeywordsLIPID BINDING PROTEIN / LIPID 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 / negative regulation of cholesterol biosynthetic process ...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 / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / positive regulation of lipoprotein transport / chylomicron remnant clearance / chylomicron remnant / maintenance of location in cell / intermediate-density lipoprotein particle / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / very-low-density lipoprotein particle clearance / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / lipid transporter activity / Chylomicron remodeling / positive regulation of cholesterol metabolic process / regulation of amyloid fibril formation / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of protein metabolic process / Chylomicron assembly / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / chylomicron / phospholipid efflux / AMPA glutamate receptor clustering / very-low-density lipoprotein particle receptor binding / lipoprotein catabolic process / multivesicular body, internal vesicle / melanosome organization / reverse cholesterol transport / high-density lipoprotein particle assembly / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / : / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / negative regulation of amyloid fibril formation / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / cholesterol catabolic process / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of axon extension / artery morphogenesis / Scavenging by Class A Receptors / negative regulation of protein metabolic process / regulation of cholesterol metabolic process / positive regulation of dendritic spine development / 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 amyloid-beta formation / locomotory exploration behavior / negative regulation of endothelial cell proliferation / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / regulation of neuronal synaptic plasticity / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of cholesterol efflux / positive regulation of dendritic spine maintenance / negative regulation of blood coagulation / negative regulation of MAP kinase activity / long-term memory / negative regulation of protein secretion / intracellular transport / fatty acid homeostasis / regulation of protein-containing complex assembly / long-chain fatty acid transport / synaptic cleft
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRupp, B. / Segelke, B.W. / Forstner, M.
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
DepositionMar 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 10, 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 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOLIPOPROTEIN E


Theoretical massNumber of molelcules
Total (without water)19,4851
Polymers19,4851
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.680, 55.590, 63.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein APOLIPOPROTEIN E / APOE3


Mass: 19485.387 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 1-165 / Mutation: TRUNCATION AT RESIDUE 165
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE MUTANT USED IN MAD PHASING EXPERIMENT
Source: (gene. exp.) Homo sapiens (human) / Strain: B834(DE)MET- / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE)MET- / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR3), VAPOR ...Details: 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR3), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
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: Apr 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: 2.49→25 Å / Num. all: 5913 / Num. obs: 5913 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 29.7
Reflection shellResolution: 2.49→2.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.245 / % possible all: 82.4
Reflection
*PLUS
Num. measured all: 39148
Reflection shell
*PLUS
% possible obs: 89.5 %

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Processing

Software
NameVersionClassification
UCSD-systemDATA REDUCTION PACKAGEdata collection
UCSD-systemDATA REDUCTION PACKAGEdata reduction
EPMRphasing
X-PLORmodel building
CCP4model building
X-PLOR3.851refinement
UCSD-systemdata scaling
X-PLORphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZ4

1bz4


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.297 544 10 %RANDOM
Rwork0.267 ---
obs-5457 89.5 %-
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-6 Å
Luzzati sigma a0.45 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 0 53 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.03
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.311.5
X-RAY DIFFRACTIONx_mcangle_it4.862
X-RAY DIFFRACTIONx_scbond_it2.182
X-RAY DIFFRACTIONx_scangle_it3.222.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 40 9.8 %
Rwork0.322 367 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PRTOPHCSDX.PRO
X-RAY DIFFRACTION2TIMETSE.TOP
X-RAY DIFFRACTION3SME_BONDS.PARAM
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.03
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: 0.373 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.322

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