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Yorodumi- PDB-1le2: STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HU... -
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-Basic information
Entry | Database: PDB / ID: 1le2 | ||||||
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Title | STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E | ||||||
Components | APOLIPOPROTEIN E2 | ||||||
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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Wilson, C. / Agard, D.A. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein. Authors: Wilson, C. / Mau, T. / Weisgraber, K.H. / Wardell, M.R. / Mahley, R.W. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1le2.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1le2.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 1le2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1le2_validation.pdf.gz | 366 KB | Display | wwPDB validaton report |
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Full document | 1le2_full_validation.pdf.gz | 375.6 KB | Display | |
Data in XML | 1le2_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1le2_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1le2 ftp://data.pdbj.org/pub/pdb/validation_reports/le/1le2 | HTTPS FTP |
-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: 16689.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: E2 / Production host: unidentified (others) / References: UniProt: P02649 |
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Compound details | THREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE APO-E2 ISOFORM DIFFERS FROM THE WILD-TYPE (E3) ...THREE ISOFORMS OF APO-E ARE RELATIVELY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: 3 Å / Lowest resolution: 10 Å / Num. obs: 2749 / % possible obs: 67.9 % |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.195 / Highest resolution: 3 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 step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 2749 / σ(I): 2 / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.7 |