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Yorodumi- EMDB-4390: Cryo-EM structure of the adenosine A2A receptor bound to a miniGs... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4390 | |||||||||
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Title | Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / DNA polymerase processivity factor activity / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / protein-disulfide reductase activity / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / cell redox homeostasis / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / positive regulation of long-term synaptic potentiation / central nervous system development / synaptic transmission, glutamatergic / positive regulation of synaptic transmission, GABAergic / locomotory behavior / positive regulation of protein secretion / astrocyte activation / apoptotic signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / 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 / G beta:gamma signalling through CDC42 / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of inflammatory response / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / vasodilation / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / blood coagulation / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / cell-cell signaling / GTPase binding / retina development in camera-type eye / presynaptic membrane / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Homo sapiens (human) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.11 Å | |||||||||
Authors | Garcia-Nafria J / Lee Y | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Elife / Year: 2018 Title: Cryo-EM structure of the adenosine A receptor coupled to an engineered heterotrimeric G protein. Authors: Javier García-Nafría / Yang Lee / Xiaochen Bai / Byron Carpenter / Christopher G Tate / Abstract: The adenosine A receptor (AR) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. Here, we determine the structure by electron cryo-microscopy (cryo-EM) ...The adenosine A receptor (AR) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. Here, we determine the structure by electron cryo-microscopy (cryo-EM) of AR at pH 7.5 bound to the small molecule agonist NECA and coupled to an engineered heterotrimeric G protein, which contains mini-G, the βγ subunits and nanobody Nb35. Most regions of the complex have a resolution of ~3.8 Å or better. Comparison with the 3.4 Å resolution crystal structure shows that the receptor and mini-G are virtually identical and that the density of the side chains and ligand are of comparable quality. However, the cryo-EM density map also indicates regions that are flexible in comparison to the crystal structures, which unexpectedly includes regions in the ligand binding pocket. In addition, an interaction between intracellular loop 1 of the receptor and the β subunit of the G protein was observed. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4390.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-4390-v30.xml emd-4390.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_4390.png | 136.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4390 | HTTPS FTP |
-Validation report
Summary document | emd_4390_validation.pdf.gz | 220.4 KB | Display | EMDB validaton report |
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Full document | emd_4390_full_validation.pdf.gz | 219.5 KB | Display | |
Data in XML | emd_4390_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4390 | HTTPS FTP |
-Related structure data
Related structure data | 6gdgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10309 (Title: Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein Data size: 1.1 TB Data #1: Unaligned multi-frame micrographs [micrographs - multiframe] Data #2: Micelle subtracted particles [picked particles - multiframe - processed] Data #3: Particles before subtraction [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4390.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Adenosine A2A receptor bound to miniGs heterotrimer
+Supramolecule #1: Adenosine A2A receptor bound to miniGs heterotrimer
+Supramolecule #2: Adenosine receptor A2a
+Supramolecule #3: miniGs heterotrimer
+Supramolecule #4: nanobody Nb35
+Macromolecule #1: TrxA,Adenosine receptor A2a
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...
+Macromolecule #5: nanobody Nb35
+Macromolecule #6: N-ETHYL-5'-CARBOXAMIDO ADENOSINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6gdg: |