+Open data
-Basic information
Entry | Database: PDB / ID: 2xtj | ||||||
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Title | The crystal structure of PCSK9 in complex with 1D05 Fab | ||||||
Components |
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Keywords | HYDROLASE/ANTIBODY / HYDROLASE-ANTIBODY COMPLEX / SERINE PROTEASE / LDL-C / LDLR / EGF-A / HYPERCHOLESTEROLEMIA | ||||||
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 / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / 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 / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / 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 / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / 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 / 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 / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / neuron differentiation / 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 / lysosome / early endosome / lysosomal membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Di Marco, S. / Volpari, C. / Carfi, A. | ||||||
Citation | Journal: J.Lipid Res. / Year: 2011 Title: A Pcsk9-Binding Antibody that Structurally Mimics the Egf(A) Domain of Ldl-Receptor Reduces Ldl Cholesterol in Vivo. Authors: Ni, Y.G. / Di Marco, S. / Condra, J.H. / Peterson, L.B. / Wang, W. / Wang, F. / Pandit, S. / Hammond, H.A. / Rosa, R. / Cummings, R.T. / Wood, D.D. / Liu, X. / Bottomley, M.J. / Shen, X. / ...Authors: Ni, Y.G. / Di Marco, S. / Condra, J.H. / Peterson, L.B. / Wang, W. / Wang, F. / Pandit, S. / Hammond, H.A. / Rosa, R. / Cummings, R.T. / Wood, D.D. / Liu, X. / Bottomley, M.J. / Shen, X. / Cubbon, R.M. / Wang, S.P. / Johns, D.G. / Volpari, C. / Hamuro, L. / Chin, J. / Huang, L. / Zhao, J.Z. / Vitelli, S. / Haytko, P. / Wisniewski, D. / Mitnaul, L.J. / Sparrow, C.P. / Hubbard, B. / Carfi, A. / Sitlani, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xtj.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xtj.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtj ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtj | HTTPS FTP |
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-Related structure data
Related structure data | 2w2mS 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
-PROPROTEIN CONVERTASE ... , 2 types, 2 molecules AP
#1: Protein | Mass: 33083.238 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#6: 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.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
-FAB FROM A HUMAN MONOCLONAL ANTIBODY, ... , 2 types, 2 molecules CE
#3: Protein | Mass: 11588.751 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN CONSTANT DOMAIN, RESIDUES 108-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli) |
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#5: Protein | Mass: 13113.582 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN CONSTANT DOMAIN, RESIDUES 132-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli) |
-Antibody , 2 types, 2 molecules BD
#2: Antibody | Mass: 11568.840 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN VARIABLE DOMAIN, RESIDUES 1-107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli) |
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#4: Antibody | Mass: 14359.157 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN VARIABLE DOMAIN, RESIDUES 1-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli) |
-Non-polymers , 2 types, 200 molecules
#7: Chemical | ChemComp-CA / |
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#8: Water | ChemComp-HOH / |
-Details
Sequence details | LEUCINE PRESENT AT A417 IN ORIGINAL CONSTRUCT. POSSIBLE NATURAL VARIANT |
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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: 2.95 Å3/Da / Density % sol: 58.34 % / Description: NONE |
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Crystal grow | Method: vapor diffusion Details: CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. ...Details: CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. FOR DATA COLLECTION CRYSTALS WERE TRANSFERRED TO A STABILIZING SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 5% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 25% PEG6000), THEN TRANSFERRED FOR 2 MIN TO A CRYOPROTECTANT SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 20% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 35% PEG6000) AND FINALLY PLACED DIRECTLY INTO LIQUID NITROGEN. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 32238 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W2M Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.58 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL MODEL CONTAINS RESIDUES 61-152 FROM THE PCSK9 PRODOMAIN (CHAIN P) AND RESIDUES 155-157 AND 178-422 FROM THE PCSK9 CATALYTIC ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL MODEL CONTAINS RESIDUES 61-152 FROM THE PCSK9 PRODOMAIN (CHAIN P) AND RESIDUES 155-157 AND 178-422 FROM THE PCSK9 CATALYTIC DOMAIN (CHAIN A) THE FINAL MODEL CONTAINS RESIDUES 1-212 FROM THE FAB LIGHT CHAIN (CHAINS B AND C)AND RESIDUES 1-236 FROM THE FAB HEAVY CHAIN (CHAINS D AND E). THERE WAS NO ELECTRON DENSITY PRESENT FOR PCSK9 RESIDUES 53-60, 153-154, 158-177 AND 423-451, NOR FOR 1D05 FAB RESIDUES 237-255 OF THE CONSTANT DOMAIN OF THE HEAVY CHAIN (CHAIN E) AND RESIDUE 213 OF THE CONSTANT DOMAIN OF THE LIGHT CHAIN (CHAIN C). THESE RESIDUES WERE THEREFORE EXCLUDED FROM THE REFINEMENT. ALL OVER THE STRUCTURE, WHEN POOR DENSITY FOR SIDE CHAINS WAS PRESENT, THE CORRESPONDING RESIDUE WAS MODELED AS ALA. ALL OVER THE STRUCTURE, WHEN POOR DENSITY FOR SIDE CHAINS WAS PRESENT, THE CORRESPONDING RESIDUE WAS MODELED AS ALA.
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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: 34.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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