+Open data
-Basic information
Entry | Database: PDB / ID: 3bps | ||||||
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Title | PCSK9:EGF-A complex | ||||||
Components |
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Keywords | HYDROLASE/Lipid Transport / PCSK9 / LDL receptor / Autocatalytic cleavage / Cholesterol metabolism / Disease mutation / Glycoprotein / Hydrolase / Lipid metabolism / Phosphoprotein / Protease / Secreted / Serine protease / Steroid metabolism / Zymogen / Coated pit / EGF-like domain / Endocytosis / Host-virus interaction / Lipid transport / Membrane / Transmembrane / Transport / HYDROLASE-Lipid Transport 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: 2.41 Å | ||||||
Authors | Kwon, H.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Molecular basis for LDL receptor recognition by PCSK9. Authors: Kwon, H.J. / Lagace, T.A. / McNutt, M.C. / Horton, J.D. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bps.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bps.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bps ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bps | HTTPS FTP |
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-Related structure data
Related structure data | 2p4eS S: Starting model for refinement |
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Similar 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: 11283.910 Da / Num. of mol.: 1 / Fragment: Prodomain, UNP residues 53-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Production host: Escherichia coli (E. coli) / Strain (production host): HEK293S References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 57443.730 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 153-692 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Production host: Escherichia coli (E. coli) / Strain (production host): HEK293S References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Protein | Mass: 9090.130 Da / Num. of mol.: 1 Fragment: EGF-like 1, EGF-like 2 domains, UNP residues 314-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Escherichia coli (E. coli) / References: UniProt: P01130 |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.49 % |
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Crystal grow | Temperature: 294 K / pH: 4.8 Details: 0.3M (NH4)H2PO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 4.80 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2007 / Details: SI |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 36583 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.8 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P4E Resolution: 2.41→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.374 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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