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- PDB-1le4: STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HU... -

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Basic information

Entry
Database: PDB / ID: 1le4
TitleSTRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E
ComponentsAPOLIPOPROTEIN E4
KeywordsLIPOPROTEIN
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 / maintenance of location in cell / 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 / acylglycerol homeostasis / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / Chylomicron remodeling / lipid transporter activity / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / response to caloric restriction / very-low-density lipoprotein particle clearance / regulation of amyloid fibril formation / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / 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 / host-mediated activation of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / 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 amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / regulation of Cdc42 protein signal transduction / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of cholesterol metabolic process / artery morphogenesis / negative regulation of protein metabolic process / regulation of axon extension / triglyceride homeostasis / Scavenging by Class A Receptors / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / positive regulation of dendritic spine development / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / response to dietary excess / antioxidant activity / locomotory exploration behavior / negative regulation of MAP kinase activity / lipoprotein particle binding / negative regulation of blood vessel endothelial cell migration / positive regulation of endocytosis / 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 / regulation of neuronal synaptic plasticity / regulation of proteasomal protein catabolic process / negative regulation of protein secretion / long-term memory / fatty acid homeostasis / long-chain fatty acid transport / regulation of protein-containing complex assembly / synaptic cleft / intracellular transport
Similarity search - Function
Apolipoprotein / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWilson, C. / Agard, D.A.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Human apolipoprotein E. Role of arginine 61 in mediating the lipoprotein preferences of the E3 and E4 isoforms.
Authors: Dong, L.M. / Wilson, C. / Wardell, M.R. / Simmons, T. / Mahley, R.W. / Weisgraber, K.H. / Agard, D.A.
#1: Journal: Science / Year: 1991
Title: Three-Dimensional Structure of the Ldl Receptor-Binding Domain of Human Apolipoprotein E
Authors: Wilson, C. / Wardell, M.R. / Weisgraber, K.H. / Mahley, R.W. / Agard, D.A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Diffraction Studies on the Amino-Terminal (Receptor-Binding) Domain of Human Apolipoprotein E3 from Serum Very Low Density Lipoproteins
Authors: Aggerbeck, L.P. / Wetterau, J.R. / Weisgraber, K.H. / Mahley, R.W. / Agard, D.A.
History
DepositionAug 22, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN E4


Theoretical massNumber of molelcules
Total (without water)16,7971
Polymers16,7971
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.710, 53.330, 85.280
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 APOLIPOPROTEIN E4


Mass: 16797.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified (others) / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE APO-E4 ISOFORM DIFFERS FROM THE WILD-TYPE (E3) ...THREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE APO-E4 ISOFORM DIFFERS FROM THE WILD-TYPE (E3) PROTEIN BY THE MUTATION CYS 112-->ARG. THE MUTANT PROTEIN SHOWS NORMAL LDL RECEPTOR BINDING BUT ALTERED LIPOPROTEIN BINDING. WHEREAS WILD-TYPE APO-E BINDS BOTH HIGH DENSITY LIPOPROTEIN (HDL) AND VERY LOW DENSITY LIPOPROTEINS (VLDL), THE APO-E4 MUTANT STRONGLY PREFERS VLDL OVER HDL. THE STRUCTURE OF TH E4 MUTANT WAS DETERMINED USING STARTING PHASES OBTAINED FRO THE E3 PROTEIN. SECONDARY STRUCTURE WAS ASSIGNED USING THE *DEFINE* PROGRAM (RICHARDS AND KUNDROT, PROTEINS V. 3, 71 (1988)).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMsodium acetate1reservior
30.2 %beta-n-glycopyranoside1reservoir
415 %PEG4001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 6752 / % possible obs: 99.1 % / Observed criterion σ(I): 2

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.175 / Highest resolution: 2.5 Å
Details: THE LOOP CONNECTING THE SECOND AND THIRD HELICES OF THE FOUR-HELIX BUNDLE (RESIDUES 83-88) IS POORLY DEFINED IN THE ELECTRON DENSITY MAP. X-PLOR-REFINED COORDINATES FOR THE LOOP HAVE BEEN ...Details: THE LOOP CONNECTING THE SECOND AND THIRD HELICES OF THE FOUR-HELIX BUNDLE (RESIDUES 83-88) IS POORLY DEFINED IN THE ELECTRON DENSITY MAP. X-PLOR-REFINED COORDINATES FOR THE LOOP HAVE BEEN INCLUDED IN THE STRUCTURE BUT ARE LIKELY TO CONTAIN ERRORS.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 101 1251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 6752 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å

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