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- PDB-1h7i: Apolipoprotein E3 22kD fragment LYS146GLN mutant -

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Basic information

Entry
Database: PDB / ID: 1h7i
TitleApolipoprotein E3 22kD fragment LYS146GLN mutant
ComponentsAPOLIPOPROTEIN E
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA
Function / homology
Function and homology information


chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle / regulation of amyloid-beta clearance / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle remodeling / Chylomicron clearance / negative regulation of triglyceride metabolic process / response to caloric restriction / acylglycerol homeostasis / NMDA glutamate receptor clustering / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / regulation of amyloid fibril formation / regulation of protein metabolic process / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / melanosome organization / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / positive regulation by host of viral process / very-low-density lipoprotein particle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / cholesterol transfer activity / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / protein import / negative regulation of blood coagulation / high-density lipoprotein particle / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / synaptic transmission, cholinergic / heparan sulfate proteoglycan binding / negative regulation of cholesterol biosynthetic process / amyloid precursor protein metabolic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / negative regulation of protein metabolic process / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding / triglyceride metabolic process / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / locomotory exploration behavior / regulation of neuronal synaptic plasticity / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / lipoprotein particle binding / positive regulation of endocytosis / antioxidant activity / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / positive regulation of cholesterol efflux / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / synaptic cleft / regulation of proteasomal protein catabolic 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: 1.9 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 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 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)22,1611
Polymers22,1611
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.700, 52.960, 84.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE FULL 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 / APOE3


Mass: 22161.031 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.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUTATION:LYS146GLN APO-E MEDIATES BINDING, INTERNALIZATION, AND CATABOLISM OF LIPOPROTEIN PARTICLES. ...MUTATION:LYS146GLN 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, 20-25% PEG 400, 1% 2-ME. RT. 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: Mar 15, 1995 / 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: 1.9→20 Å / Num. obs: 14706 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.0413 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2 / % possible all: 96.6

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Processing

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

1bz4


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.224 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.158 / 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 AND 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 EXCESSIVE B-FACTORS >100 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
Rfree0.259 737 5 %RANDOM
Rwork0.203 ---
obs0.205 13960 98.3 %-
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: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 134 1284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0211175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.6791.9741576
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_restr0.1740.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021295
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.3320
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2980.581
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.38
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.712697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.07831110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.733478
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7224466
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: 1.9→1.92 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rfree0.273 33
Rwork0.311 498

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