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- PDB-7fcs: Crystal structure of the N-terminal domain of mutants of Human Ap... -

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Basic information

Entry
Database: PDB / ID: 7fcs
TitleCrystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
ComponentsApolipoprotein E
KeywordsLIPID TRANSPORT / Apolipoproteins / lipid binding
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 / 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 / maintenance of location in cell / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / Chylomicron remodeling / lipid transporter activity / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / 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 / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / AMPA glutamate receptor clustering / lipoprotein catabolic process / multivesicular body, internal vesicle / melanosome organization / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / Scavenging by Class A Receptors / triglyceride metabolic process / positive regulation of dendritic spine development / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / negative regulation of blood vessel endothelial cell migration / regulation of neuronal synaptic plasticity / 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 / negative regulation of MAP kinase activity / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCherakara, S. / Kumar, A. / Garai, K. / Ghosh, B.
CitationJournal: To be published
Title: Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
Authors: Cherakara, S. / Kumar, A. / Garai, K. / Ghosh, B.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3814
Polymers22,3121
Non-polymers693
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-31 kcal/mol
Surface area8120 Å2
Unit cell
Length a, b, c (Å)40.870, 53.493, 85.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 22312.238 Da / Num. of mol.: 1 / Mutation: C130V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Plasmid: pET32a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P02649
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.46 % / Mosaicity: 0.24 °
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.15 / Details: 100 mM sodium cacodylate, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 15, 2021 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→45.39 Å / Num. obs: 25447 / % possible obs: 99.6 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Net I/σ(I): 20.4 / Num. measured all: 120391 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.634.80.699604512610.7310.3490.7842.1100
8.76-45.393.80.0356871830.9950.0220.04244.994.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GS9

1gs9


Resolution: 1.6→25.89 Å / SU ML: 0.1665 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 1283 5.05 %
Rwork0.1881 24105 -
obs0.1896 25388 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 3 118 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811164
X-RAY DIFFRACTIONf_angle_d1.03421567
X-RAY DIFFRACTIONf_chiral_restr0.0478173
X-RAY DIFFRACTIONf_plane_restr0.0126204
X-RAY DIFFRACTIONf_dihedral_angle_d3.8306167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.30661360.26862658X-RAY DIFFRACTION100
1.66-1.740.25571430.22972621X-RAY DIFFRACTION99.89
1.74-1.830.27731510.19742646X-RAY DIFFRACTION99.82
1.83-1.950.21291390.1862660X-RAY DIFFRACTION99.79
1.95-2.10.23441470.20142643X-RAY DIFFRACTION99.47
2.1-2.310.19621410.1662654X-RAY DIFFRACTION99.11
2.31-2.640.18021510.16382672X-RAY DIFFRACTION99.4
2.64-3.330.21011270.20132729X-RAY DIFFRACTION99.37
3.33-25.890.22161480.18522822X-RAY DIFFRACTION98.64

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