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- PDB-8ce0: N-terminal domain of human apolipoprotein E -

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Basic information

Entry
Database: PDB / ID: 8ce0
TitleN-terminal domain of human apolipoprotein E
ComponentsMaltodextrin-binding protein,Apolipoprotein E
KeywordsLIPID TRANSPORT / Apolipoprotein E / N-terminal domain
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 / carbohydrate transmembrane transporter activity / 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
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
Maltodextrin-binding protein / Apolipoprotein E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMarek, M. / Nemergut, 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
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 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

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2102
Polymers75,1181
Non-polymers921
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint0 kcal/mol
Surface area8410 Å2
Unit cell
Length a, b, c (Å)45.529, 53.085, 73.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltodextrin-binding protein,Apolipoprotein E / Apo-E


Mass: 75117.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, NCTC8450_00456, NCTC9775_03059, APOE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376KDN7, UniProt: P02649
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 / Details: NaCl, Hepes, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.75→45.53 Å / Num. obs: 18525 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 981 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→38.657 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 918 4.98 %0
Rwork0.1903 ---
obs0.1915 18451 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→38.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 6 133 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151216
X-RAY DIFFRACTIONf_angle_d1.2271634
X-RAY DIFFRACTIONf_dihedral_angle_d8.431063
X-RAY DIFFRACTIONf_chiral_restr0.072178
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.84230.32471360.29862448X-RAY DIFFRACTION100
1.8423-1.95770.32351250.27022447X-RAY DIFFRACTION100
1.9577-2.10890.24441180.20532489X-RAY DIFFRACTION100
2.1089-2.32110.2311160.19212494X-RAY DIFFRACTION100
2.3211-2.65680.21271340.18162494X-RAY DIFFRACTION100
2.6568-3.34710.22561350.19442527X-RAY DIFFRACTION100
3.3471-38.6570.18391540.16932634X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.5657 Å / Origin y: 41.8505 Å / Origin z: 49.8125 Å
111213212223313233
T0.2314 Å2-0.015 Å2-0.0137 Å2-0.2257 Å20.0008 Å2--0.2197 Å2
L1.0056 °2-0.8676 °20.5154 °2-1.5427 °2-0.3554 °2--0.9017 °2
S-0.1278 Å °-0.0669 Å °0.0262 Å °0.2167 Å °0.0201 Å °-0.0854 Å °-0.0813 Å °-0.0097 Å °-0.0102 Å °
Refinement TLS groupSelection details: all

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