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- PDB-7kfa: PCSK9 in complex with PCSK9i a 13mer cyclic peptide LDLR disruptor -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kfa | ||||||
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Title | PCSK9 in complex with PCSK9i a 13mer cyclic peptide LDLR disruptor | ||||||
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![]() | LIPID TRANSPORT / HYDROLASE / PRO-PROTEIN CONVERTASE / CORONARY HEART DISEASE / HYPERCHOLESTEROLEMIA / LOW DENSITY LIPOPROTEIN RECEPTOR / AUTOCATALYTIC CLEAVAGE / CHOLESTEROL METABOLISM / DISEASE MUTATION / GLYCOPROTEIN / LIPID METABOLISM / PHOSPHORYLATION / PROTEASE / SECRETED / SERINE PROTEASE / STEROID METABOLISM / ZYMOGEN | ||||||
Function / homology | ![]() 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 / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...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 / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / signaling receptor inhibitor activity / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / low-density lipoprotein particle receptor binding / triglyceride metabolic process / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / kidney development / cholesterol homeostasis / Post-translational protein phosphorylation / neuron differentiation / 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 / late endosome / lysosome / early endosome / endoplasmic reticulum lumen / lysosomal membrane / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / RNA binding / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chopra, R. / Xu, M. / Spraggon, G. | ||||||
![]() | ![]() Title: Identification of a PCSK9-LDLR disruptor peptide with in vivo function. Authors: Brousseau, M.E. / Clairmont, K.B. / Spraggon, G. / Flyer, A.N. / Golosov, A.A. / Grosche, P. / Amin, J. / Andre, J. / Burdick, D. / Caplan, S. / Chen, G. / Chopra, R. / Ames, L. / Dubiel, D. ...Authors: Brousseau, M.E. / Clairmont, K.B. / Spraggon, G. / Flyer, A.N. / Golosov, A.A. / Grosche, P. / Amin, J. / Andre, J. / Burdick, D. / Caplan, S. / Chen, G. / Chopra, R. / Ames, L. / Dubiel, D. / Fan, L. / Gattlen, R. / Kelly-Sullivan, D. / Koch, A.W. / Lewis, I. / Li, J. / Liu, E. / Lubicka, D. / Marzinzik, A. / Nakajima, K. / Nettleton, D. / Ottl, J. / Pan, M. / Patel, T. / Perry, L. / Pickett, S. / Poirier, J. / Reid, P.C. / Pelle, X. / Seepersaud, M. / Subramanian, V. / Vera, V. / Xu, M. / Yang, L. / Yang, Q. / Yu, J. / Zhu, G. / Monovich, L.G. #1: ![]() Title: The self-inhibited structure of full-length PCSK9 at 1.9 A reveals structural homology with resistin within the C-terminal domain. Authors: Hampton, E.N. / Knuth, M.W. / Li, J. / Harris, J.L. / Lesley, S.A. / Spraggon, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 97.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kevC ![]() 2qtwS S: Starting model for refinement C: citing same article ( |
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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: 14019.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 58272.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Protein/peptide | Mass: 1633.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20.0% PEG-6000, 0.1M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→57.67 Å / Num. obs: 23342 / % possible obs: 94.2 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.096 / Rrim(I) all: 0.096 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3405 / CC1/2: 0.784 / Rpim(I) all: 0.335 / Rrim(I) all: 0.665 / % possible all: 78.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QTW Resolution: 2.45→57.67 Å / SU ML: 0.2931 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7678 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→57.67 Å
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Refine LS restraints |
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LS refinement shell |
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