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Yorodumi- PDB-6e4y: Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9, un... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e4y | ||||||
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Title | Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Hydrolase / PCSK9 / FAB complex | ||||||
Function / homology | Function and homology information 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 / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / positive regulation of receptor internalization / apolipoprotein binding / 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 / early endosome / lysosome / immune response / 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 / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Ultsch, M.H. / Kirchhofer, D.K. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 Title: Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain. Authors: Ultsch, M. / Li, W. / Eigenbrot, C. / Di Lello, P. / Lipari, M.T. / Gerhardy, S. / AhYoung, A.P. / Quinn, J. / Franke, Y. / Chen, Y. / Kong Beltran, M. / Peterson, A. / Kirchhofer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e4y.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e4y.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 6e4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e4y ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e4y | HTTPS FTP |
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-Related structure data
Related structure data | 6e4zC 6mv5C 1qygS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 2468.516 Da / Num. of mol.: 1 / Fragment: UNP residues 32-53 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NBP7 |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24255.182 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4 |
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#2: Antibody | Mass: 24040.912 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4 / References: UniProt: A0A097PUG4 |
-Non-polymers , 3 types, 138 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% w/v PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 30008 / % possible obs: 99 % / Redundancy: 5.9 % / Biso Wilson estimate: 54.58 Å2 / CC1/2: 0.824 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Rrim(I) all: 0.078 / Χ2: 1.001 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.24→2.33 Å / Redundancy: 6 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 2967 / CC1/2: 0.824 / Rpim(I) all: 0.304 / Rrim(I) all: 0.749 / Χ2: 0.981 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QYG Resolution: 2.24→48.01 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.196
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Displacement parameters | Biso mean: 70.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.24→48.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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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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