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Yorodumi- PDB-5ndd: Crystal structure of a thermostabilised human protease-activated ... -
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-Basic information
Entry | Database: PDB / ID: 5ndd | ||||||
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Title | Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at 2.8 angstrom resolution | ||||||
Components | Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / 7TM | ||||||
Function / homology | Function and homology information positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway ...positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway / thrombin-activated receptor activity / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of actin filament depolymerization / cell-cell junction maintenance / positive regulation of cytokine production involved in immune response / positive regulation of toll-like receptor 4 signaling pathway / T cell activation involved in immune response / positive regulation of pseudopodium assembly / negative regulation of chemokine production / positive regulation of phagocytosis, engulfment / positive regulation of chemotaxis / negative regulation of JNK cascade / neutrophil activation / establishment of endothelial barrier / regulation of canonical NF-kappaB signal transduction / positive regulation of positive chemotaxis / positive regulation of leukocyte chemotaxis / positive regulation of Rho protein signal transduction / leukocyte migration / pseudopodium / regulation of blood coagulation / positive regulation of interleukin-10 production / regulation of JNK cascade / negative regulation of tumor necrosis factor-mediated signaling pathway / G-protein alpha-subunit binding / negative regulation of insulin secretion / positive regulation of chemokine production / viral release from host cell by cytolysis / peptidoglycan catabolic process / Peptide ligand-binding receptors / positive regulation of superoxide anion generation / positive regulation of GTPase activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / G protein-coupled receptor activity / electron transport chain / positive regulation of JNK cascade / vasodilation / G-protein beta-subunit binding / positive regulation of interleukin-6 production / positive regulation of type II interferon production / blood coagulation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / protease binding / host cell cytoplasm / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / early endosome / positive regulation of cell migration / defense response to bacterium / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / innate immune response / signaling receptor binding / heme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / plasma membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å | ||||||
Authors | Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. ...Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.-O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N. | ||||||
Citation | Journal: Nature / Year: 2017 Title: Structural insight into allosteric modulation of protease-activated receptor 2. Authors: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / ...Authors: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ndd.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ndd.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ndd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ndd_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 5ndd_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 5ndd_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 5ndd_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndd ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndd | HTTPS FTP |
-Related structure data
Related structure data | 5ndzC 5nj6C 3vw7S 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
#1: Protein | Mass: 69558.898 Da / Num. of mol.: 1 Mutation: G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A,I289A, L293A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: e, T4Tp126, F2RL1, GPR11, PAR2, cybC / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: D9IEF7, UniProt: P55085, UniProt: P0ABE7, UniProt: P00720*PLUS, lysozyme |
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#2: Chemical | ChemComp-8TZ / (~{ |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.52 % / Description: Needle-shaped crystals (on average 0.1mm long) |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.8 Details: 0.1 M sodium citrate/citrate acid pH 5.5-6.2, 0.2 M ammonium phosphate dibasic, 38-43 % (w/v) PEG400 and 1 mM AZ8838 PH range: 5.5-6.2 / Temp details: Constant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→34.34 Å / Num. obs: 17995 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.11 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2671 / CC1/2: 0.692 / Rpim(I) all: 0.522 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VW7 Resolution: 2.801→34.336 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→34.336 Å
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Refine LS restraints |
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LS refinement shell |
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