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- PDB-8ax9: Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P2... -

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Basic information

Entry
Database: PDB / ID: 8ax9
TitleHuman Apolipoprotein E4 (ApoE4) N-terminal domain (space group P212121)
ComponentsMaltose/maltodextrin-binding periplasmic protein,Apolipoprotein E
KeywordsLIPID BINDING PROTEIN / Apolipoprotein E
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 / maintenance of location in cell ...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 / maintenance of location in cell / regulation of amyloid-beta clearance / negative regulation of cholesterol biosynthetic process / 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 / Chylomicron clearance / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of low-density lipoprotein particle receptor catabolic process / response to caloric restriction / cellular response to lipoprotein particle stimulus / lipid transporter activity / very-low-density lipoprotein particle clearance / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / regulation of amyloid fibril formation / lipoprotein catabolic process / AMPA glutamate receptor clustering / high-density lipoprotein particle remodeling / 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 / high-density lipoprotein particle assembly / low-density lipoprotein particle / host-mediated activation of viral process / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / protein import / very-low-density lipoprotein particle / cholesterol catabolic process / heparan sulfate proteoglycan binding / low-density lipoprotein particle remodeling / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / regulation of Cdc42 protein signal transduction / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / regulation of amyloid precursor protein catabolic process / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of cholesterol metabolic process / artery morphogenesis / regulation of axon extension / negative regulation of protein metabolic process / Scavenging by Class A Receptors / triglyceride homeostasis / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / detection of maltose stimulus / negative regulation of endothelial cell proliferation / positive regulation of dendritic spine development / maltose transport complex / response to dietary excess / antioxidant activity / negative regulation of MAP kinase activity / carbohydrate transport / negative regulation of amyloid-beta formation / lipoprotein particle binding / locomotory exploration behavior / negative regulation of long-term synaptic potentiation / positive regulation of endocytosis / negative regulation of blood vessel endothelial cell migration / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of dendritic spine maintenance / carbohydrate transmembrane transporter activity / regulation of neuronal synaptic plasticity / maltose binding / positive regulation of cholesterol efflux / negative regulation of protein secretion / maltose transport / maltodextrin transmembrane transport
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: 1.549 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 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
Water2,972165
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 area8260 Å2
Unit cell
Length a, b, c (Å)45.593, 53.175, 73.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 165 / 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: 1.549→45.59 Å / Num. obs: 26880 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 23.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.5812.21.813240.5180.5551.96699.8
8.48-45.5910.10.0192090.9990.0060.0299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS9

5gs9


Resolution: 1.549→38.805 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 1287 4.8 %
Rwork0.1843 25534 -
obs0.1848 26821 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.13 Å2 / Biso mean: 32.0036 Å2 / Biso min: 14.09 Å2
Refinement stepCycle: final / Resolution: 1.549→38.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 166 1339
Biso mean---39.08 -
Num. residues----143
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.549-1.6110.31691280.27732824
1.611-1.68440.22661430.22662764
1.6844-1.77320.25611360.2152802
1.7732-1.88430.19831330.19832817
1.8843-2.02970.20881520.18852787
2.0297-2.2340.18181540.16382821
2.234-2.55720.20471500.17072838
2.5572-3.22150.18981360.18682877
3.2215-38.8050.181550.17643004
Refinement TLS params.Method: refined / Origin x: 17.5567 Å / Origin y: 42.151 Å / Origin z: 50.2105 Å
111213212223313233
T0.1537 Å2-0.0097 Å2-0.0228 Å2-0.1446 Å2-0.0049 Å2--0.1398 Å2
L0.5063 °2-0.5519 °20.1628 °2-1.227 °2-0.2368 °2--0.6539 °2
S-0.1216 Å °-0.0537 Å °0.0005 Å °0.2052 Å °0.0264 Å °-0.1039 Å °-0.1142 Å °-0.0115 Å °-0.0117 Å °
Refinement TLS groupSelection details: (chain A and resseq 23:165)

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