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Yorodumi- PDB-3p5c: The structure of the LDLR/PCSK9 complex reveals the receptor in a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p5c | ||||||
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Title | The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation | ||||||
Components |
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Keywords | HYDROLASE/LIPID BINDING PROTEIN / B-propellor / Receptor / Convertase / HYDROLASE-LIPID BINDING PROTEIN complex | ||||||
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 / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / receptor-mediated endocytosis involved in cholesterol transport ...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 / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / PCSK9-AnxA2 complex / low-density lipoprotein particle receptor activity / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / response to caloric restriction / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / high-density lipoprotein particle clearance / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / low-density lipoprotein particle / phospholipid transport / cholesterol transport / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / negative regulation of amyloid fibril formation / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / negative regulation of protein metabolic process / artery morphogenesis / triglyceride metabolic process / cellular response to fatty acid / regulation of cholesterol metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / amyloid-beta clearance / lipoprotein particle binding / sorting endosome / apolipoprotein binding / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / long-term memory / phagocytosis / regulation of neuron apoptotic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / receptor-mediated endocytosis / liver development / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / lipid metabolic process / neuron differentiation / positive regulation of inflammatory response / endocytosis / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / 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 / lysosomal membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Lo Surdo, P. / Bottomley, M.J. / Calzetta, A. / Settembre, E.C. / Cirillo, A. / Pandit, S. / Ni, Y. / Hubbard, B. / Sitlani, A. / Carfi, A. | ||||||
Citation | Journal: Embo Rep. / Year: 2011 Title: Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. Authors: Lo Surdo, P. / Bottomley, M.J. / Calzetta, A. / Settembre, E.C. / Cirillo, A. / Pandit, S. / Ni, Y.G. / Hubbard, B. / Sitlani, A. / Carfi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p5c.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p5c.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 3p5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p5c ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p5c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10490.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Protein | Mass: 57371.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
#3: Protein | Mass: 49271.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q59FQ1, UniProt: P01130*PLUS | ||
#4: Chemical | ChemComp-CA / Sequence details | A AND P CHAINS COME FROM THE SAME PROPROTEIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 0.1M imidazole, 0.7M sodium acetate pH 7.0, VAPOR DIFFUSION, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2010 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→60 Å / Num. all: 33296 / Num. obs: 33321 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 4.2→4.43 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 4783 / Rsym value: 0.63 / % possible all: 48.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.2→4.35 Å
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