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Yorodumi- PDB-1f5y: NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BIND... -
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-Basic information
Entry | Database: PDB / ID: 1f5y | ||||||
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Title | NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR | ||||||
Components | LOW-DENSITY LIPOPROTEIN RECEPTORLDL receptor | ||||||
Keywords | LIPID BINDING PROTEIN / Beta hairpin / 3-10 helix / calcium binding | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination | ||||||
Authors | Kurniawan, N.D. / Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Smith, R. | ||||||
Citation | 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. / Bieri, S. / Brown, C.J. / Brereton, I.M. / Kroon, P.A. / Smith, R. #1: Journal: Biochemistry / Year: 1998 Title: Calcium is Essential for the Structural Integrity of the Cysteine-Rich, Ligand-Binding Repeat of the Low-Density Lipoprotein Receptor Authors: Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Lee, H.T. / Smith, R. #2: Journal: Biochemistry / Year: 1998 Title: Folding, Calcium Binding, and Structural Characterization of a Concatemer of the First and Second Ligand-Binding Modules of the Low-Density Lipoprotein Receptor Authors: Bieri, S. / Atkins, A.R. / Lee, H.T. / Winzor, D.J. / Smith, R. / Kroon, P.A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Three-Dimensional Structure of a Cysteine-Rich Repeat from the Low-Density Lipoprotein Receptor Authors: Daly, N.L. / Scanlon, M.J. / Djordjevic, J.T. / Kroon, P.A. / Smith, R. #4: Journal: Biochemistry / Year: 1995 Title: Three-Dimensional Structure of the Second Cysteine-Rich Repeat from the Human Low-Density Lipoprotein Receptor Authors: Daly, N.L. / Djordjevic, J.T. / Kroon, P.A. / Smith, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f5y.cif.gz | 468.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f5y.ent.gz | 404.4 KB | Display | PDB format |
PDBx/mmJSON format | 1f5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f5y ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f5y | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9258.997 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING MODULES 1-2 Source method: isolated from a genetically manipulated source Details: LIGAND-BINDING MODULE CONCATEMER / Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Production host: Escherichia coli (E. coli) / 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: This structure was determined using standard 2D homonuclear techniques |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 0.045 / pH: 5.5 / Pressure: atmospheric atm / Temperature: 310 K | |||||||||
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: Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination Software ordinal: 1 Details: NMR inputs: NOE total 889: 286 intra, 273 sequential, 184 medium, 146 long range; Others: 32 dihedral restraints, 13 h-bonds, 12 calcium coordination | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |