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- PDB-1ea8: Apolipoprotein E3 22kD fragment LYS146GLU mutant -

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Basic information

Entry
Database: PDB / ID: 1ea8
TitleApolipoprotein E3 22kD fragment LYS146GLU mutant
ComponentsAPOLIPOPROTEIN E
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA
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 / maintenance of location in cell / 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 / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / Chylomicron remodeling / response to caloric restriction / very-low-density lipoprotein particle clearance / lipid transporter activity / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of amyloid fibril formation / Chylomicron assembly / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / high-density lipoprotein particle remodeling / lipoprotein catabolic process / AMPA glutamate receptor clustering / 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 / host-mediated activation of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / protein import / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / regulation of Cdc42 protein signal transduction / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / regulation of axon extension / artery morphogenesis / triglyceride homeostasis / Scavenging by Class A Receptors / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / positive regulation of dendritic spine development / negative regulation of endothelial cell proliferation / negative regulation of amyloid-beta formation / response to dietary excess / locomotory exploration behavior / antioxidant activity / negative regulation of MAP kinase activity / lipoprotein particle binding / negative regulation of blood vessel endothelial cell migration / positive regulation of endocytosis / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of dendritic spine maintenance / negative regulation of blood coagulation / positive regulation of cholesterol efflux / regulation of neuronal synaptic plasticity / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / long-chain fatty acid transport / regulation of protein-containing complex assembly / synaptic cleft / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRupp, B. / Peters-Libeu, C. / Verderame, J.
CitationJournal: To be Published
Title: Apolipoprotein E3 22Kd Fragment Lys146Gln Mutant
Authors: Rupp, B. / Peters-Libeu, C. / Verderame, J.
History
DepositionJul 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)22,1621
Polymers22,1621
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.797, 53.473, 84.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE NATIVE PROTEIN CONTAINING THE N-TERMINAL 22KD LDLRECEPTOR BINDING DOMAIN (1-191) AND THE C-TERMINAL 10KDLIPID BINDING DOMAIN (192-299) FORMS A TETRAMER IN VIVO

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Components

#1: Protein APOLIPOPROTEIN E


Mass: 22162.016 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 1-191 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / 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
Compound detailsCHAIN A ENGINEERED MUTATION LYS146GLU APO-E MEDIATES BINDING, INTERNALIZATION, AND CATABOLISM OF ...CHAIN A ENGINEERED MUTATION LYS146GLU APO-E MEDIATES BINDING, INTERNALIZATION, AND CATABOLISM OF LIPOPROTEIN PARTICLES. IT CAN SERVE AS A LIGAND FOR THE LDL(APO B/E) RECEPTOR AND FOR THE SPECIFIC APO-E RECEPTOR (CHYLOMICRON REMNANT) OF HEPATIC TISSUES.

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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: 43.9 %
Crystal growpH: 5.6
Details: 50MM NA-CACODYLATE, PH 5.6, ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2).

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: ADSC ADSC MULTIWIRE / Date: Sep 15, 1994 / Details: COLLIMATOR 0.5 MM
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 13284 / % possible obs: 94.3 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.36
Reflection shellResolution: 1.95→2.13 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 1.43 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
ADSCdata reduction
ADSCdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZ4

1bz4


Resolution: 1.95→24.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.112 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-22 AND 163-191 ARE ABSENT IN MODEL AND IN ELECTRON DENSITY THE N- AND C-TERMINI ARE DISORDERED IN APOE 22KD FRAGMENTS. THE N- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-22 AND 163-191 ARE ABSENT IN MODEL AND IN ELECTRON DENSITY THE N- AND C-TERMINI ARE DISORDERED IN APOE 22KD FRAGMENTS. THE N-TERMINAL MAIN CHAIN LIKELY SPLITS AT RESIDUE 22. SOME PARTIALLY OCCUPIED SOLVENT MOLECULES IN CLOSE PROXIMITY MAY IN FACT BE POORLY LOCALIZED FRAGMENTS OF THE ABSENT TERMINII. LOOP REGION 82-89 IS COMMONLY DISORDERED IN APOE MODELS. DENSITY IS POOR AND THE LOOP BACKBONE WAS MODELLED AFTER 1BZ4 AND IS LIKELY PRESENT IN MULTIPLE CONFORMATIONS. THE AUTHORS CAUTION THAT A NUMBER OF LOOP SIDE CHAIN ATOMS HAVE HIGH B-FACTORS AND ARE PROBABLY NOT LOCALISED AT ALL. THE MOLECULE IS GENERALLY VERY FLEXIBLE IN THE LOOP DOMAIN AND HAS OVERALL HIGH B VALUES IN MOST MODELS. SEE SEGELKE ET AL PROT SCI 9:886-897 (2000) FOR THE BIOLOGICAL RELEVANCE OF FLEXIBILITY IN LIPID BINDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 658 5 %RANDOM
Rwork0.236 ---
obs0.237 12626 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.95→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 133 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7341.981587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.3566
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.584
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.324
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2992697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42831112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4863487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9744475
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.98 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rfree0.451 21
Rwork0.361 447

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