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

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Basic information

Entry
Database: PDB / ID: 7fcr
TitleCrystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
ComponentsApolipoprotein E
KeywordsLIPID TRANSPORT / Apolipoprotein / 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 / 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 / very-low-density lipoprotein particle clearance / lipid transporter activity / 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 / host-mediated activation of viral process / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / protein import / high-density lipoprotein particle / 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 / negative regulation of endothelial cell proliferation / positive regulation of dendritic spine development / response to dietary excess / antioxidant activity / negative regulation of MAP kinase activity / negative regulation of amyloid-beta formation / lipoprotein particle binding / locomotory exploration behavior / negative regulation of long-term synaptic potentiation / negative regulation of blood vessel endothelial cell migration / positive regulation of endocytosis / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / positive regulation of cholesterol efflux / negative regulation of protein secretion / fatty acid homeostasis / long-term memory / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport / positive regulation of lipid biosynthetic process
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: 1.4 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)22,3723
Polymers22,3261
Non-polymers462
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-18 kcal/mol
Surface area8280 Å2
Unit cell
Length a, b, c (Å)40.642, 53.207, 85.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: 22326.264 Da / Num. of mol.: 1 / Mutation: C130I
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.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.08 Å3/Da / Density % sol: 40.92 % / Mosaicity: 0.19 °
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: 1.4→45.24 Å / Num. obs: 37333 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 26.1 / Num. measured all: 267298 / Scaling rejects: 4
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
1.4-1.427.20.941297118030.7090.3731.0122.299.7
7.67-45.245.40.03815002760.9970.0180.04255.997.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1gs9


Resolution: 1.4→25.82 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 1829 4.91 %
Rwork0.1706 35439 -
obs0.1717 37268 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.7 Å2 / Biso mean: 27.6874 Å2 / Biso min: 13.68 Å2
Refinement stepCycle: final / Resolution: 1.4→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 2 138 1252
Biso mean--32.96 36.32 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.440.2831380.2352653279199
1.44-1.480.21781430.17972651279499
1.48-1.530.19921450.14072675282099
1.53-1.580.16621330.13572684281799
1.58-1.650.18221410.13992686282799
1.65-1.720.18951570.145726782835100
1.72-1.810.20481200.145427232843100
1.81-1.920.20321440.1527232867100
1.92-2.070.19961450.161227222867100
2.07-2.280.19191410.154727452886100
2.28-2.610.19081390.155527692908100
2.61-3.290.19251470.187528022949100
3.29-25.820.19011360.18692928306499

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