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- PDB-1lpe: THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF... -

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Basic information

Entry
Database: PDB / ID: 1lpe
TitleTHREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF HUMAN APOLIPOPROTEIN E
ComponentsAPOLIPOPROTEIN E3
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 / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant ...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 / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / lipoprotein particle / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / intermediate-density lipoprotein particle / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / Chylomicron clearance / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of low-density lipoprotein particle receptor catabolic process / very-low-density lipoprotein particle clearance / cellular response to lipoprotein particle stimulus / Chylomicron assembly / lipoprotein biosynthetic process / response to caloric restriction / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / high-density lipoprotein particle remodeling / positive regulation of amyloid-beta clearance / triglyceride metabolic process / reverse cholesterol transport / very-low-density lipoprotein particle / regulation of amyloid fibril formation / positive regulation of cholesterol metabolic process / high-density lipoprotein particle assembly / low-density lipoprotein particle / host-mediated activation of viral process / multivesicular body, internal vesicle / melanosome organization / high-density lipoprotein particle / cholesterol transfer activity / amyloid precursor protein metabolic process / protein import / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / regulation of behavioral fear response / heparan sulfate proteoglycan binding / negative regulation of endothelial cell migration / positive regulation of membrane protein ectodomain proteolysis / regulation of Cdc42 protein signal transduction / regulation of amyloid precursor protein catabolic process / cholesterol efflux / HDL remodeling / regulation of axon extension / regulation of cholesterol metabolic process / triglyceride homeostasis / Scavenging by Class A Receptors / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / virion assembly / regulation of innate immune response / positive regulation of dendritic spine development / negative regulation of endothelial cell proliferation / antioxidant activity / synaptic transmission, cholinergic / lipid carrier activity / positive regulation of lipoprotein transport / negative regulation of platelet-derived growth factor receptor signaling pathway / locomotory exploration behavior / negative regulation of amyloid-beta formation / lipoprotein particle binding / negative regulation of blood vessel endothelial cell migration / AMPA glutamate receptor clustering / negative regulation of platelet activation / negative regulation of long-term synaptic potentiation / cholesterol metabolic process / regulation of neuronal synaptic plasticity / negative regulation of blood coagulation / positive regulation of cholesterol efflux / fatty acid homeostasis / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / regulation of protein-containing complex assembly / positive regulation of endocytosis / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / Nuclear signaling by ERBB4 / nitric oxide-cGMP-mediated signaling / long-term memory / Retinoid metabolism and transport / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of MAPK cascade / cytoskeleton organization / endocytic vesicle lumen
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: 2.25 Å
AuthorsWilson, C. / Agard, D.A.
Citation
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.
#1: 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 E3


Theoretical massNumber of molelcules
Total (without water)16,7431
Polymers16,7431
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.650, 53.960, 85.430
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 E3


Mass: 16743.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE STRUCTURE WAS SOLVED USING THE MOST FREQUENTLY ...THREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE STRUCTURE WAS SOLVED USING THE MOST FREQUENTLY OCCURRING ISOFORM, APO-E3. 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.2 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %PEG4001reservior
320 mMsodium acetate-acid1reservoir
40.2 %beta-n-octylglucopyranoside1reservoir
50.1 %beta-mercaptoethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 6899 / Num. measured all: 17129 / Rmerge(I) obs: 0.054

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.175 / Highest resolution: 2.25 Å
Details: X-RAY DATA WAS COLLECTED AT -150OC TO MINIMIZE RADIATION DECAY. PHASE INFORMATION WAS PROVIDED BY ISOMORPHOUS AND ANOMALOUS DIFFERENCES MEASURED FOR THE DIMETHYL MERCURY DERIVATIVE. ...Details: X-RAY DATA WAS COLLECTED AT -150OC TO MINIMIZE RADIATION DECAY. PHASE INFORMATION WAS PROVIDED BY ISOMORPHOUS AND ANOMALOUS DIFFERENCES MEASURED FOR THE DIMETHYL MERCURY DERIVATIVE. EXTENSIVE SOLVENT FLATTENING (B.C. WANG PROGRAMS) WAS USED TO REFINE THE PHASES PRIOR TO BUILDING AN ATOMIC MODEL. 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: 2.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 121 1293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.2
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
Rfactor Rwork: 0.175 / Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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