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- PDB-8ax8: Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P3121) -

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Basic information

Entry
Database: PDB / ID: 8ax8
TitleHuman Apolipoprotein E4 (ApoE4) N-terminal domain (space group P3121)
ComponentsMaltose/maltodextrin-binding periplasmic protein,Apolipoprotein E
KeywordsLIPID BINDING PROTEIN / Apolipoprotein E
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 / detection of maltose stimulus / maltose transport complex / 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 / carbohydrate transport / positive regulation of endocytosis / antioxidant activity / response to dietary excess / negative regulation of blood vessel endothelial cell migration / carbohydrate transmembrane transporter activity / maltose binding / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / maltose transport / maltodextrin transmembrane transport / negative regulation of platelet activation / positive regulation of cholesterol efflux / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion
Similarity search - Function
Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Apolipoprotein E / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.551 Å
AuthorsNemergut, M. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: Mol Neurodegener / Year: 2023
Title: Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer's Disease drug candidate.
Authors: Nemergut, M. / Marques, S.M. / Uhrik, L. / Vanova, T. / Nezvedova, M. / Gadara, D.C. / Jha, D. / Tulis, J. / Novakova, V. / Planas-Iglesias, J. / Kunka, A. / Legrand, A. / Hribkova, H. / ...Authors: Nemergut, M. / Marques, S.M. / Uhrik, L. / Vanova, T. / Nezvedova, M. / Gadara, D.C. / Jha, D. / Tulis, J. / Novakova, V. / Planas-Iglesias, J. / Kunka, A. / Legrand, A. / Hribkova, H. / Pospisilova, V. / Sedmik, J. / Raska, J. / Prokop, Z. / Damborsky, J. / Bohaciakova, D. / Spacil, Z. / Hernychova, L. / Bednar, D. / Marek, M.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Apolipoprotein E


Theoretical massNumber of molelcules
Total (without water)75,1181
Polymers75,1181
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8190 Å2
Unit cell
Length a, b, c (Å)47.693, 47.693, 104.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Apolipoprotein E / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Apo-E


Mass: 75117.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: K12 / Gene: malE, b4034, JW3994, APOE / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.55→41.3 Å / Num. obs: 20733 / % possible obs: 99.8 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.3
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 991 / CC1/2: 0.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS9

5gs9


Resolution: 1.551→38.425 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 975 4.72 %
Rwork0.1984 19700 -
obs0.2 20675 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.33 Å2 / Biso mean: 32.4923 Å2 / Biso min: 13.9 Å2
Refinement stepCycle: final / Resolution: 1.551→38.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 0 105 1227
Biso mean---38.29 -
Num. residues----135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.551-1.63280.2951220.2662739
1.6328-1.73510.27261300.24412781
1.7351-1.8690.25381240.21592796
1.869-2.05710.21381470.2012793
2.0571-2.35480.2531580.18612774
2.3548-2.96660.23081580.20112829
2.9666-38.4250.2151360.18872988
Refinement TLS params.Method: refined / Origin x: -27.7516 Å / Origin y: 13.0893 Å / Origin z: -7.3952 Å
111213212223313233
T0.11 Å2-0.0008 Å20.0192 Å2-0.1793 Å20.0251 Å2--0.1403 Å2
L2.2619 °2-0.7376 °2-0.1358 °2-0.7683 °20.1922 °2--0.9893 °2
S-0.117 Å °-0.2503 Å °-0.2017 Å °0.1064 Å °0.082 Å °0.0115 Å °0.1075 Å °0.0279 Å °-0.003 Å °
Refinement TLS groupSelection details: (chain A and resseq 24:163)

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