+Open data
-Basic information
Entry | Database: PDB / ID: 4py0 | ||||||
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Title | Crystal structure of P2Y12 receptor in complex with 2MeSATP | ||||||
Components | P2Y purinoceptor 12, Soluble cytochrome b562 | ||||||
Keywords | MEMBRANE PROTEIN / purinergic receptor P2Y12 / partial agonist-bound / G-protein coupled receptor (GPCR) / signaling protein-nucleotide complex / PSI-Biology / GPCR Network / Structural Genomics / signaling membrane protein / GPCR / platelet activation / membrane | ||||||
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: 3.1 Å | ||||||
Authors | Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. ...Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q. / GPCR Network (GPCR) | ||||||
Citation | Journal: Nature / Year: 2014 Title: Agonist-bound structure of the human P2Y12 receptor Authors: Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / ...Authors: Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4py0.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4py0.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 4py0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4py0_validation.pdf.gz | 948.3 KB | Display | wwPDB validaton report |
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Full document | 4py0_full_validation.pdf.gz | 961 KB | Display | |
Data in XML | 4py0_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4py0_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/4py0 ftp://data.pdbj.org/pub/pdb/validation_reports/py/4py0 | HTTPS FTP |
-Related structure data
Related structure data | 4pxzSC 1m6tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 53248.879 Da / Num. of mol.: 1 / Mutation: D294N, M1007W, H1102I, R1106L Source method: isolated from a genetically manipulated source Details: Chimera protein of N-terminal residues 2-223 from P2Y12R (P2Y12_HUMAN), Soluble cytochrome b562 (C562_ECOLX), and C-terminal residues 224-342 from P2Y12R (P2Y12_HUMAN). Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: HORK3, P2RY12, cybC / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q9H244, UniProt: P0ABE7 | ||
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#2: Chemical | ChemComp-6AT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 35-40% PEG 400, 0.15-0.20M ammonium tartrate, 4% v/v MPD, 0.1M sodium citrate, pH 6.0, Lipidic cubic phase (LCP), temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2013 / Details: mirrors |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 8273 / % possible obs: 92.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 87.79 Å2 / Rmerge(I) obs: 0.222 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.2 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4PXZ and 1M6T Resolution: 3.1→28.81 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.8638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.498
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Displacement parameters | Biso mean: 88.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.653 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→28.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.47 Å / Total num. of bins used: 5
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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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