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Open data
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Basic information
Entry | Database: PDB / ID: 2w2n | ||||||
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Title | WT PCSK9-deltaC bound to EGF-A H306Y mutant of LDLR | ||||||
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![]() | HYDROLASE/RECEPTOR / HYDROLASE-RECEPTOR COMPLEX / PCSK9 / LDLR / PROPROTEIN CONVERTASE / LOW-DENSITY LIPOPROTEIN RECEPTOR / EGF / CARDIOVASCULAR DISEASE / FAMILIAL HYPERCHOLESTEROLEMIA / LIPID METABOLISM / SERINE PROTEASE / HYDROLASE / LIPID TRANSPORT / STEROID METABOLISM / RECEPTOR | ||||||
Function / homology | ![]() 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 / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / 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 / 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 / signaling receptor inhibitor activity / amyloid-beta clearance by cellular catabolic process / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / phospholipid transport / negative regulation of low-density lipoprotein receptor activity / cholesterol transport / low-density lipoprotein particle / 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 / cellular response to fatty acid / regulation of cholesterol metabolic process / low-density lipoprotein particle receptor binding / triglyceride metabolic process / amyloid-beta clearance / COPII-coated ER to Golgi transport vesicle / sorting endosome / lipoprotein particle binding / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / cellular response to low-density lipoprotein particle stimulus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / long-term memory / phospholipid metabolic process / 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 / kidney development / cholesterol homeostasis / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / neuron differentiation / lipid metabolic process / positive regulation of inflammatory response / endocytosis / cellular response to insulin stimulus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / positive regulation of neuron apoptotic process / 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 / endoplasmic reticulum lumen Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. ...Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A. | ||||||
![]() | ![]() Title: Structural and Biochemical Characterization of the Wild Type Pcsk9/Egf-Ab Complex and Natural Fh Mutants. Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. ...Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.2 KB | Display | ![]() |
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Full document | ![]() | 413.2 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w2mC ![]() 2w2oC ![]() 2w2pC ![]() 2w2qC ![]() 2qtwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33108.227 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||||
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#2: Protein | Mass: 12120.479 Da / Num. of mol.: 1 / Fragment: EGF-A DOMAIN, RESIDUES 314-393 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Protein | Mass: 12679.604 Da / Num. of mol.: 1 / Fragment: PRODOMAIN, RESIDUES 53-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES IN THE SEQUENCE ABOVE ARE A CLONING ARTEFACT, A ...HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES IN THE SEQUENCE ABOVE ARE A CLONING ARTEFACT, A LINKER AND A 6HIS TAG. HUMAN LDLR EGF-AB DOMAIN. THE FIRST 27 RESIDUES IN THE SEQUENCE ABOVE ARE A CLONING ARTEFACT, A 6HIS TAG AND A LINKER. HUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ABOVE ARE A CLONING ARTEFACT. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES PH 7.5, 10% (W/V) PEG 8000, 8% (V/V) ETHYLENE GLYCOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45 Å / Num. obs: 33566 / % possible obs: 98.1 % / Observed criterion σ(I): 3.5 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QTW Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.342 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.177 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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