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- EMDB-33504: Cryo-EM structure of the purinergic receptor P2Y12R in complex wi... -
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Open data
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Basic information
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Title | Cryo-EM structure of the purinergic receptor P2Y12R in complex with 2MeSADP and Gi | ||||||||||||||||||
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![]() | G protein-coupled receptor / purinergic receptor / P2Y12R / Ligand binding / signal transduction / MEMBRANE PROTEIN | ||||||||||||||||||
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 / positive regulation of monoatomic ion transport ...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 / regulation of chemotaxis / positive regulation of urine volume / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / cell projection organization / negative regulation of adenylate cyclase activity / positive regulation of neural precursor cell proliferation / gamma-aminobutyric acid signaling pathway / positive regulation of ruffle assembly / negative regulation of synaptic transmission / 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 / response to nutrient / positive regulation of insulin receptor signaling pathway / positive regulation of superoxide anion generation / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / establishment of localization in cell / Regulation of insulin secretion / 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-coupled acetylcholine receptor signaling pathway / G-protein activation / 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 / platelet aggregation / 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 / 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 / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / midbody / G alpha (i) signalling events / cell body / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
Images | ![]() | 40.3 KB | ||
Others | ![]() ![]() | 49.5 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xxiMC ![]() 7xxhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33504_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33504_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : The purinergic receptor P2Y12R in complex with 2MeSADP and Gi
Entire | Name: The purinergic receptor P2Y12R in complex with 2MeSADP and Gi |
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Components |
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-Supramolecule #1: The purinergic receptor P2Y12R in complex with 2MeSADP and Gi
Supramolecule | Name: The purinergic receptor P2Y12R in complex with 2MeSADP and Gi type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: P2Y purinoceptor 12
Macromolecule | Name: P2Y purinoceptor 12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 43.665078 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAPQAVDNLT SAPGNTSLCT RDYKITQVLF PLLYTVLFFV GLITNGLAMR IFFQIRSKSN FIIFLKNTVI SDLLMILTFP FKILSDAKL GTGPLRTFVC QVTSVIFYFT MYISISFLGL ITIDRYQKTT RPFKTSNPKN LLGAKILSVV IWAFMFLLSL P NMILTNRQ ...String: GAPQAVDNLT SAPGNTSLCT RDYKITQVLF PLLYTVLFFV GLITNGLAMR IFFQIRSKSN FIIFLKNTVI SDLLMILTFP FKILSDAKL GTGPLRTFVC QVTSVIFYFT MYISISFLGL ITIDRYQKTT RPFKTSNPKN LLGAKILSVV IWAFMFLLSL P NMILTNRQ PRDKNVKKCS FLKSEFGLVW HEIVNYICQV IFWINFLIVI VCYTLITKEL YRSYVRTRGV GKVPRKKVNV KV FIIIAVF FICFVPFHFA RIPYTLSQTR DVFDCTAENT LFYVKESTLW LTSLNACLDP FIYFFLCKSF RNSLISMLKC PNS ATSLSQ DNRKKEQDGG DPNEETPMEF LEVLFQGPGS WSHPQFEKGS GAGASAGSWS HPQFEK UniProtKB: P2Y purinoceptor 12 |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-2
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-2 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.502863 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGCTVSAEDK AAAERSKMID KNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEDG YSEEECRQYR AVVYSNTIQS IMAIVKAMG NLQIDFADPS RADDARQLFA LSCTAEEQGV LPDDLSGVIR RLWADHGVQA CFGRSREYQL NDSAAYYLND L ERIAQSDY ...String: MGCTVSAEDK AAAERSKMID KNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEDG YSEEECRQYR AVVYSNTIQS IMAIVKAMG NLQIDFADPS RADDARQLFA LSCTAEEQGV LPDDLSGVIR RLWADHGVQA CFGRSREYQL NDSAAYYLND L ERIAQSDY IPTQQDVLRT RVKTTGIVET HFTFKDLHFK MFDVGAQRSE RKKWIHCFEG VTAIIFCVAL SAYDLVLAED EE MNRMHAS MKLFDSICNN KWFTDTSIIL FLNKKDLFEE KITHSPLTIC FPEYTGANKY DEAASYIQSK FEDLNKRKDT KEI YTHFTC STDTKNVQFV FDAVTDVIIK NNLKDCGLF UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-2 |
-Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 38.245805 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG ...String: MHHHHHHSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CF FPNGNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADRAGVLAGH DNR VSCLGV TDDGMAVATG SWDSFLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #5: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)
Macromolecule | Name: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) type: ligand / ID: 5 / Number of copies: 1 / Formula: 6AD |
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Molecular weight | Theoretical: 473.293 Da |
Chemical component information | ![]() ChemComp-6AD: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 858424 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |