[English] 日本語
Yorodumi- PDB-1f8z: NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f8z | ||||||
---|---|---|---|---|---|---|---|
Title | NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR | ||||||
Components | LOW-DENSITY LIPOPROTEIN RECEPTORLDL receptor | ||||||
Keywords | LIPID BINDING PROTEIN / LDL receptor / ligand-binding domain / calcium-binding / familial hypercholesterolemia | ||||||
Function / homology | Function and homology information regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / response to caloric restriction / negative regulation of microglial cell activation / Chylomicron clearance / PCSK9-LDLR complex ...regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / response to caloric restriction / negative regulation of microglial cell activation / Chylomicron clearance / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / high-density lipoprotein particle clearance / lipoprotein catabolic process / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / regulation of protein metabolic process / low-density lipoprotein particle / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / negative regulation of amyloid fibril formation / phospholipid transport / cholesterol transport / endolysosome membrane / negative regulation of protein metabolic process / artery morphogenesis / regulation of cholesterol metabolic process / cellular response to fatty acid / lipoprotein particle binding / amyloid-beta clearance / sorting endosome / cellular response to low-density lipoprotein particle stimulus / long-term memory / Retinoid metabolism and transport / phagocytosis / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / apical part of cell / Clathrin-mediated endocytosis / amyloid-beta binding / basolateral plasma membrane / protease binding / lysosome / molecular adaptor activity / receptor complex / early endosome / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Method | SOLUTION NMR / Structure determination by Torsion angle dynamics, Molecular dynamics | ||||||
Authors | Clayton, D.J. / Brereton, I.M. / Kroon, P.A. / Smith, R. | ||||||
Citation | Journal: FEBS Lett. / Year: 2000 Title: Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities. Authors: Clayton, D. / Brereton, I.M. / Kroon, P.A. / Smith, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1f8z.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1f8z.ent.gz | 189.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f8z ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f8z | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 4392.759 Da / Num. of mol.: 1 / Fragment: SIXTH LIGAND-BINDING MODULE / Source method: obtained synthetically / Details: Peptide synthesis - based on the human sequence / References: UniProt: P01130 |
---|---|
#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 10 mM / pH: 5.50 / Pressure: 1 atm / Temperature: 298 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: Structure determination by Torsion angle dynamics, Molecular dynamics Software ordinal: 1 Details: Structures are based on 552 distance constraints, 18 backbone angle restraints and 14 sidechain angle restraints | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |