+Open data
-Basic information
Entry | Database: PDB / ID: 5oca | |||||||||
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Title | PCSK9:Fab Complex with Dextran Sulfate | |||||||||
Components |
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Keywords | HYDROLASE / PROTEIN FAB COMPLEX / AUTOCATALYTIC CLEAVAGE / CHOLESTEROL METABOLISM / DISEASE MUTATION / DISULFIDE BOND / GLYCOPROTEIN / LIPID METABOLISM / PHOSPHOPROTEIN / PROTEASE / SECRETED / SERINE PROTEASE / STEROID METABOLISM / ZYMOGEN / HYDROLASE-IMMUNE SYSTEM 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 / neurogenesis / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / liver development / kidney development / cholesterol homeostasis / Post-translational protein phosphorylation / cellular response to insulin stimulus / neuron differentiation / 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 / endoplasmic reticulum lumen / serine-type endopeptidase activity / lysosomal membrane / apoptotic process / perinuclear region of cytoplasm / cell surface / Golgi apparatus / endoplasmic reticulum / RNA binding / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Thirup, S.S. / Vilstrup, J.P. | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Heparan sulfate proteoglycans present PCSK9 to the LDL receptor. Authors: Gustafsen, C. / Olsen, D. / Vilstrup, J. / Lund, S. / Reinhardt, A. / Wellner, N. / Larsen, T. / Andersen, C.B.F. / Weyer, K. / Li, J.P. / Seeberger, P.H. / Thirup, S. / Madsen, P. / Glerup, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oca.cif.gz | 228.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oca.ent.gz | 178.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oca_validation.pdf.gz | 918.7 KB | Display | wwPDB validaton report |
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Full document | 5oca_full_validation.pdf.gz | 941.5 KB | Display | |
Data in XML | 5oca_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 5oca_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/5oca ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5oca | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-Proprotein convertase subtilisin/kexin type ... , 2 types, 2 molecules AB
#1: Protein | Mass: 14107.839 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 57328.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 25489.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#4: Antibody | Mass: 22626.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Sugars , 1 types, 1 molecules
#5: Polysaccharide | 2,3,4-tri-O-sulfo-beta-D-altropyranose-(1-6)-2,3-di-O-sulfo-alpha-L-glucopyranose / Heparan sulfate disaccharide |
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-Non-polymers , 2 types, 790 molecules
#6: Chemical | #7: 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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.1 M Tris-HCl, 0.2 M Sodium acetate, 10-15% PEG 4000, 3-6% Dextran sodium salt (Mr 5000), pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-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 315 / Detector: CCD / Date: Jun 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 107766 / % possible obs: 99.9 % / Redundancy: 3.5 % / Net I/σ(I): 11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.287 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→38.287 Å
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Refine LS restraints |
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LS refinement shell |
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