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Yorodumi- PDB-7pp1: Crystal structure of the P2Y12 receptor in complex with the inver... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pp1 | ||||||
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Title | Crystal structure of the P2Y12 receptor in complex with the inverse agonist selatogrel. | ||||||
Components | P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12 | ||||||
Keywords | MEMBRANE PROTEIN / Inverse agonist / complex | ||||||
Function / homology | Function and homology information visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration ...visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration / G protein-coupled adenosine receptor activity / hemostasis / cell projection membrane / regulation of chemotaxis / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / cell projection organization / positive regulation of ruffle assembly / positive regulation of cell adhesion mediated by integrin / lamellipodium assembly / cellular response to ATP / response to axon injury / monoatomic ion transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / establishment of localization in cell / electron transport chain / calcium-mediated signaling / platelet activation / platelet aggregation / ADP signalling through P2Y purinoceptor 12 / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / cell surface / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Mac Sweeney, A. / Tidten-Luksch, N. | ||||||
Funding support | 1items
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Citation | Journal: Biochem Pharmacol / Year: 2022 Title: Inverse agonist efficacy of selatogrel blunts constitutive P2Y12 receptor signaling by inducing the inactive receptor conformation. Authors: Pons, V. / Garcia, C. / Tidten-Luksch, N. / Mac Sweeney, A. / Caroff, E. / Gales, C. / Riederer, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pp1.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pp1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pp1_validation.pdf.gz | 921.9 KB | Display | wwPDB validaton report |
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Full document | 7pp1_full_validation.pdf.gz | 928.1 KB | Display | |
Data in XML | 7pp1_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7pp1_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/7pp1 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/7pp1 | HTTPS FTP |
-Related structure data
Related structure data | 4ntjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53248.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with ...Details: P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3 Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: P2RY12, HORK3, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H244, UniProt: P0ABE7 |
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#2: Chemical | ChemComp-7Y5 / |
#3: Chemical | ChemComp-CLR / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase Details: 0.1 M ammonium formate, 0.1 M sodium cacdylate, pH 6.0-6.5, 25-35% PEG400 PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→78.7 Å / Num. obs: 16554 / % possible obs: 98.9 % / Redundancy: 50.8 % / CC1/2: 0.99 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.78→2.87 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1494 / CC1/2: 0.5 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ntj Resolution: 2.78→45.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.218 / SU B: 20.968 / SU ML: 0.377 / Average fsc free: 0.7527 / Average fsc work: 0.769 / Cross valid method: FREE R-VALUE / ESU R: 0.674 / ESU R Free: 0.366 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.413 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→45.68 Å
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Refine LS restraints |
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LS refinement shell |
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