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- PDB-7xxi: Cryo-EM structure of the purinergic receptor P2Y12R in complex wi... -
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Basic information
Entry | Database: PDB / ID: 7xxi | ||||||||||||||||||
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Title | Cryo-EM structure of the purinergic receptor P2Y12R in complex with 2MeSADP and Gi | ||||||||||||||||||
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![]() | MEMBRANE PROTEIN / G protein-coupled receptor / purinergic receptor / P2Y12R / Ligand binding / signal transduction | ||||||||||||||||||
Function / homology | ![]() 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 / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / : ...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 / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / : / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration / G protein-coupled adenosine receptor activity / hemostasis / G protein-coupled adenosine receptor signaling pathway / negative regulation of calcium ion-dependent exocytosis / cell projection membrane / positive regulation of urine volume / regulation of chemotaxis / positive regulation of chemotaxis / negative regulation of adenylate cyclase activity / substrate-dependent cell migration, cell extension / cell projection organization / positive regulation of neural precursor cell proliferation / gamma-aminobutyric acid signaling pathway / negative regulation of synaptic transmission / positive regulation of ruffle assembly / positive regulation of cell adhesion mediated by integrin / lamellipodium assembly / cellular response to ATP / neuronal dense core vesicle / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / response to axon injury / Adenylate cyclase inhibitory pathway / monoatomic ion transport / positive regulation of insulin receptor signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to nutrient / guanyl-nucleotide exchange factor activity / positive regulation of superoxide anion generation / Regulation of insulin secretion / establishment of localization in cell / G protein-coupled receptor binding / calcium-mediated signaling / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / platelet activation / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / platelet aggregation / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / midbody / cell body / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Ras protein signal transduction Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||||||||
![]() | Tan, Q. / Li, B. / Han, S. / Zhao, Q. / Wu, B. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into signal transduction of the purinergic receptors P2Y1R and P2Y12R. Authors: Beibei Li / Shuo Han / Mu Wang / Yu Yu / Limin Ma / Xiaojing Chu / Qiuxiang Tan / Qiang Zhao / Beili Wu / ![]() | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 178.3 KB | Display | ![]() |
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PDB format | ![]() | 131.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33504MC ![]() 7xxhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 43665.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 40502.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 38245.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Chemical | ChemComp-6AD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The purinergic receptor P2Y12R in complex with 2MeSADP and Gi Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 858424 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.03 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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