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- PDB-7fcr: Crystal structure of the N-terminal domain of mutants of Human Ap... -
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Basic information
Entry | Database: PDB / ID: 7fcr | ||||||
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Title | Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) | ||||||
![]() | Apolipoprotein E | ||||||
![]() | LIPID TRANSPORT / Apolipoprotein / lipid binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Cherakara, S. / Kumar, A. / Garai, K. / Ghosh, B. | ||||||
![]() | ![]() Title: Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) Authors: Cherakara, S. / Kumar, A. / Garai, K. / Ghosh, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.1 KB | Display | ![]() |
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Full document | ![]() | 423 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fcsC ![]() 1gs9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22326.264 Da / Num. of mol.: 1 / Mutation: C130I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.92 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 5.15 / Details: 100 mM sodium cacodylate, 28% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 15, 2021 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→45.24 Å / Num. obs: 37333 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 26.1 / Num. measured all: 267298 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GS9 Resolution: 1.4→25.82 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.7 Å2 / Biso mean: 27.6874 Å2 / Biso min: 13.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→25.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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