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- PDB-6v7m: Crystal structure of a proteolytically cleaved, amino terminal do... -

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Basic information

Entry
Database: PDB / ID: 6v7m
TitleCrystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3
Components(Apolipoprotein E) x 2
KeywordsLIPID TRANSPORT / proteolysis / Alzheimers / lipid / lipoprotein / lipids / disease
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 / 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 / regulation of proteasomal protein catabolic process
Similarity search - Function
Apolipoprotein A/E / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
PHOSPHATE ION / Apolipoprotein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcPherson, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3.
Authors: McPherson, A.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein E
B: Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3293
Polymers21,2342
Non-polymers951
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: prepared from natural source - human serum
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-35 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.330, 54.450, 86.670
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 Apolipoprotein E / Apo-E


Mass: 11812.354 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Production host: Homo sapiens (human) / References: UniProt: P02649
#2: Protein Apolipoprotein E / Apo-E


Mass: 9421.833 Da / Num. of mol.: 1 / Fragment: UNP residues 101-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Production host: Homo sapiens (human) / References: UniProt: P02649
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Crystallization was by sitting drop vapor diffusion in Cryschem plates at room temperature. Reservoirs were 16% to 18 % 2-methyl-2,4-pentanediol (MPD) buffered with 0.1 M sodium acetate at ...Details: Crystallization was by sitting drop vapor diffusion in Cryschem plates at room temperature. Reservoirs were 16% to 18 % 2-methyl-2,4-pentanediol (MPD) buffered with 0.1 M sodium acetate at pH 5.8 and including 0.25% octyl-beta-D-1-thioglucopyranoside. The droplets were initial composed of equal amounts of the reservoir and an 8 mg/ml solution of the protein in 0.02 M ammonium carbonate.
PH range: 5.8 - 6.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1993
RadiationMonochromator: Supper graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→46.33 Å / Num. obs: 11748 / % possible obs: 86 % / Redundancy: 3.8 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.127 / Rrim(I) all: 0.277 / Rsym value: 0.24 / Net I/σ(I): 3.9
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 207 / CC1/2: 0.096 / Rpim(I) all: 0.528 / Rrim(I) all: 0.747

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
SDMSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NFN

1nfn


Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.414 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.197
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 572 5 %RANDOM
Rwork0.2025 ---
obs0.2054 10817 82.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 194.46 Å2 / Biso mean: 49.084 Å2 / Biso min: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---1.92 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 5 82 1292
Biso mean--94.82 47.93 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131250
X-RAY DIFFRACTIONr_bond_other_d00.0181194
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.6511682
X-RAY DIFFRACTIONr_angle_other_deg1.2081.5852756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1575152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88220.57587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7071518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021402
X-RAY DIFFRACTIONr_gen_planes_other00.02284
LS refinement shellResolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 11 -
Rwork0.441 174 -
all-185 -
obs--18.74 %
Refinement TLS params.Method: refined / Origin x: 24.0876 Å / Origin y: 39.3224 Å / Origin z: 59.014 Å
111213212223313233
T0.0376 Å2-0.0064 Å20.0165 Å2-0.1289 Å2-0.0056 Å2--0.0111 Å2
L1.0419 °2-0.429 °2-1.1919 °2-0.9472 °20.4546 °2--1.3723 °2
S-0.0522 Å °-0.0512 Å °-0.0576 Å °0.1852 Å °-0.0121 Å °0.0825 Å °0.0542 Å °0.0902 Å °0.0643 Å °

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