+Open data
-Basic information
Entry | Database: PDB / ID: 1ea8 | ||||||
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Title | Apolipoprotein E3 22kD fragment LYS146GLU mutant | ||||||
Components | APOLIPOPROTEIN E | ||||||
Keywords | LIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA | ||||||
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 blood vessel endothelial cell migration / 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 / positive regulation of cholesterol efflux / 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 / long-chain fatty acid transport / 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 long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Rupp, B. / Peters-Libeu, C. / Verderame, J. | ||||||
Citation | Journal: To be Published Title: Apolipoprotein E3 22Kd Fragment Lys146Gln Mutant Authors: Rupp, B. / Peters-Libeu, C. / Verderame, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ea8.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ea8.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 1ea8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ea8_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 1ea8_full_validation.pdf.gz | 420.6 KB | Display | |
Data in XML | 1ea8_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1ea8_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/1ea8 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/1ea8 | HTTPS FTP |
-Related structure data
Related structure data | 1h7iC 1bz4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THE NATIVE PROTEIN CONTAINING THE N-TERMINAL 22KD LDLRECEPTOR BINDING DOMAIN (1-191) AND THE C-TERMINAL 10KDLIPID BINDING DOMAIN (192-299) FORMS A TETRAMER IN VIVO |
-Components
#1: Protein | Mass: 22162.016 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 1-191 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P02649 |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION LYS146GLU APO-E MEDIATES BINDING, INTERNALIZATION, AND CATABOLISM OF ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | pH: 5.6 Details: 50MM NA-CACODYLATE, PH 5.6, ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2). |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 |
Detector | Type: ADSC ADSC MULTIWIRE / Date: Sep 15, 1994 / Details: COLLIMATOR 0.5 MM |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 13284 / % possible obs: 94.3 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 1.95→2.13 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 1.43 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BZ4 Resolution: 1.95→24.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.112 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-22 AND 163-191 ARE ABSENT IN MODEL AND IN ELECTRON DENSITY THE N- AND C-TERMINI ARE DISORDERED IN APOE 22KD FRAGMENTS. THE N- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-22 AND 163-191 ARE ABSENT IN MODEL AND IN ELECTRON DENSITY THE N- AND C-TERMINI ARE DISORDERED IN APOE 22KD FRAGMENTS. THE N-TERMINAL MAIN CHAIN LIKELY SPLITS AT RESIDUE 22. SOME PARTIALLY OCCUPIED SOLVENT MOLECULES IN CLOSE PROXIMITY MAY IN FACT BE POORLY LOCALIZED FRAGMENTS OF THE ABSENT TERMINII. LOOP REGION 82-89 IS COMMONLY DISORDERED IN APOE MODELS. DENSITY IS POOR AND THE LOOP BACKBONE WAS MODELLED AFTER 1BZ4 AND IS LIKELY PRESENT IN MULTIPLE CONFORMATIONS. THE AUTHORS CAUTION THAT A NUMBER OF LOOP SIDE CHAIN ATOMS HAVE HIGH B-FACTORS AND ARE PROBABLY NOT LOCALISED AT ALL. THE MOLECULE IS GENERALLY VERY FLEXIBLE IN THE LOOP DOMAIN AND HAS OVERALL HIGH B VALUES IN MOST MODELS. SEE SEGELKE ET AL PROT SCI 9:886-897 (2000) FOR THE BIOLOGICAL RELEVANCE OF FLEXIBILITY IN LIPID BINDING.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→24.92 Å
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Refine LS restraints |
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