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Yorodumi- PDB-1i0u: SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-H... -
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-Basic information
Entry | Database: PDB / ID: 1i0u | ||||||
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Title | SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR | ||||||
Components | LOW DENSITY LIPOPROTEIN RECEPTOR | ||||||
Keywords | LIPID BINDING PROTEIN / anti-parallel beta strands / calcium binding sites | ||||||
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 / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling ...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 / negative regulation of microglial cell activation / 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 / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / intestinal cholesterol absorption / low-density lipoprotein particle binding / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / cholesterol transport / low-density lipoprotein particle / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / amyloid-beta clearance / sorting endosome / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / 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 / Cargo recognition for clathrin-mediated endocytosis / late endosome / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / 1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation | ||||||
Authors | Kurniawan, N.D. / Aliabadizadeh, K. / Brereton, I.M. / Kroon, P.A. / Smith, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: NMR structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-density lipoprotein receptor. Authors: Kurniawan, N.D. / Aliabadizadeh, K. / Brereton, I.M. / Kroon, P.A. / Smith, R. #1: Journal: Protein Sci. / Year: 2000 Title: NMR Structure of a Concatemer of the First and Second Ligand-Binding Modules of the Human Low-Density Lipoprotein Receptor Authors: Kurniawan, N.D. / Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Smith, R. #2: Journal: J.Mol.Biol. / Year: 1998 Title: An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An ...Title: An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components Authors: Springer, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i0u.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i0u.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i0u_validation.pdf.gz | 294.7 KB | Display | wwPDB validaton report |
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Full document | 1i0u_full_validation.pdf.gz | 294.5 KB | Display | |
Data in XML | 1i0u_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1i0u_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/1i0u ftp://data.pdbj.org/pub/pdb/validation_reports/i0/1i0u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9001.013 Da / Num. of mol.: 1 / Fragment: EGF-AB CONCATEMER(RESIDUES 314-395) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PGEX-4T; PET-30A+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA; BL21-DE3 / References: UniProt: P01130 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 15N T1, T2, and NOE relaxations to obtain backbone dynamics information T1/T2 data were not used for structure refinement |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz |
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-Processing
NMR software |
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Refinement | Method: 1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation Software ordinal: 1 Details: The structures are based on: 874 NOE restraints, 64 phi dihedral angles, 14 chi1 dihedral angles, 14 hydrogen bonds, 9 calcium ion ligand restraints | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Energy minimised average structure from 30 selected structure with lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 1 |