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Yorodumi- PDB-1lpe: THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpe | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF HUMAN APOLIPOPROTEIN E | ||||||
Components | APOLIPOPROTEIN E3 | ||||||
Keywords | LIPOPROTEIN | ||||||
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 / 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 / lipid transporter activity / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / cholesterol transfer activity / positive regulation by host of viral process / reverse cholesterol transport / very-low-density lipoprotein particle / positive regulation of amyloid-beta clearance / 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 / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / negative regulation of cholesterol biosynthetic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / amyloid precursor protein metabolic process / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of protein metabolic process / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / locomotory exploration behavior / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / regulation of neuronal synaptic plasticity / positive regulation of endocytosis / lipoprotein particle binding / 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 / intracellular transport / positive regulation of cholesterol efflux / 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 / regulation of proteasomal protein catabolic process / synaptic cleft Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Wilson, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpe.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpe.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpe ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
Compound details | THREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE STRUCTURE WAS SOLVED USING THE MOST FREQUENTLY ...THREE ISOFORMS OF APO-E ARE RELATIVELY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 7.2 / PH range high: 4.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 6899 / Num. measured all: 17129 / Rmerge(I) obs: 0.054 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor 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 step | Cycle: LAST / Highest resolution: 2.25 Å
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Refine LS restraints |
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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 |