+Open data
-Basic information
Entry | Database: PDB / ID: 8yh2 | ||||||
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Title | A3R-Gi complex bound to adenosine | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GPCR / adenosine receptor / complex / G protein | ||||||
Function / homology | Function and homology information Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G protein-coupled adenosine receptor activity / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G protein-coupled adenosine receptor activity / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (i) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 / response to peptide hormone / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / clathrin-dependent endocytosis of virus by host cell / G alpha (q) signalling events / Extra-nuclear estrogen signaling / host cell surface receptor binding / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / fusion of virus membrane with host plasma membrane / GTPase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / virion attachment to host cell / GTP binding / nucleolus Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) Homo sapiens (human) Influenza A virus Ovis aries (sheep) Human orthopneumovirus Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | ||||||
Authors | Oshima, H.S. / Shihoya, W. / Nureki, O. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Structural insights into the agonist selectivity and structure-based engineering of the adenosine A3 receptor Authors: Oshima, H.S. / Ogawa, A. / Sano, F.K. / Akasaka, H. / Kawakami, T. / Okamoto, H.H. / Iwama, A. / Nagiri, C. / Wei, F.-Y. / Shihoya, W. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yh2.cif.gz | 231 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yh2.ent.gz | 166.3 KB | Display | PDB format |
PDBx/mmJSON format | 8yh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yh2_validation.pdf.gz | 910.7 KB | Display | wwPDB validaton report |
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Full document | 8yh2_full_validation.pdf.gz | 923.3 KB | Display | |
Data in XML | 8yh2_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 8yh2_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/8yh2 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yh2 | HTTPS FTP |
-Related structure data
Related structure data | 39279MC 8yh3C 8yh5C 8yh6C M: map data used to model this data C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 40586.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Gene: GNB1 / Production host: Homo sapiens (human) / References: UniProt: P62871 | ||||||||||
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#2: Protein | Mass: 48846.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2, GNAI1 / Production host: Homo sapiens (human) / References: UniProt: P59768, UniProt: P63096 #3: Protein | | Mass: 88315.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2)), (gene. exp.) Ovis aries (sheep), (gene. exp.) Human orthopneumovirus Strain: A/Victoria/3/1975(H3N2) / Gene: HA, ADORA3 / Production host: Homo sapiens (human) References: UniProt: P03435, UniProt: W5QED6, UniProt: A0A5P9VSM6 #4: Antibody | | Mass: 27720.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #5: Chemical | ChemComp-ADN / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: A3R-Gi complex bound to adenosine / Type: COMPLEX / Entity ID: #1, #3, #2, #4 / Source: RECOMBINANT |
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Source (natural) | Organism: Ovis aries (sheep) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160357 / Symmetry type: POINT |