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Yorodumi- EMDB-23390: Allosteric modulator LY3154207 binding to SKF-81297-bound dopamin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23390 | |||||||||||||||
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Title | Allosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein | |||||||||||||||
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Sample |
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Function / homology | Function and homology information dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / sensitization / operant conditioning / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / dopamine binding / heterotrimeric G-protein binding ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / sensitization / operant conditioning / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / dopamine binding / heterotrimeric G-protein binding / G protein-coupled receptor complex / peristalsis / regulation of dopamine metabolic process / grooming behavior / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of neuron migration / habituation / dopamine transport / positive regulation of potassium ion transport / astrocyte development / conditioned taste aversion / striatum development / dentate gyrus development / maternal behavior / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / arrestin family protein binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / non-motile cilium / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / 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 (i) signalling events / long-term synaptic depression / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / alkylglycerophosphoethanolamine phosphodiesterase activity / mating behavior / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / adult walking behavior / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / ciliary membrane / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / G protein-coupled dopamine receptor signaling pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / temperature homeostasis / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / D-glucose import / transmission of nerve impulse / dopamine metabolic process / PKA activation in glucagon signalling / behavioral response to cocaine / hair follicle placode formation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral fear response / developmental growth / neuronal action potential / photoreceptor outer segment / G-protein alpha-subunit binding / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / Hedgehog 'off' state / prepulse inhibition / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / GABA-ergic synapse / cardiac muscle cell apoptotic process Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (cattle) / Lama glama (llama) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Zhuang Y / Krumm B / Zhang H / Zhou XE / Wang Y / Guo J / Huang X-P / Liu Y / Wang L / Cheng X ...Zhuang Y / Krumm B / Zhang H / Zhou XE / Wang Y / Guo J / Huang X-P / Liu Y / Wang L / Cheng X / Jiang Y / Jiang H / Melcher K / Zhang C / Yi W / Roth BL / Zhang Y / Xu HE | |||||||||||||||
Funding support | China, United States, 4 items
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Citation | Journal: Cell Res / Year: 2021 Title: Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor. Authors: Youwen Zhuang / Brian Krumm / Huibing Zhang / X Edward Zhou / Yue Wang / Xi-Ping Huang / Yongfeng Liu / Xi Cheng / Yi Jiang / Hualiang Jiang / Cheng Zhang / Wei Yi / Bryan L Roth / Yan Zhang / H Eric Xu / #1: Journal: Biorxiv / Year: 2021 Title: Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor Authors: Zhuang Y / Krumm B / Zhang H / Zhou XE / Wang Y / Guo J / Huang X-P / Liu Y / Wang L / Cheng X / Jiang Y / Jiang H / Melcher K / Zhang C / Yi W / Roth BL / Zhang Y / Xu HE | |||||||||||||||
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_23390.map.gz | 19.3 MB | EMDB map data format | |
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Header (meta data) | emd-23390-v30.xml emd-23390.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_23390.png | 66.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23390 | HTTPS FTP |
-Validation report
Summary document | emd_23390_validation.pdf.gz | 338.2 KB | Display | EMDB validaton report |
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Full document | emd_23390_full_validation.pdf.gz | 337.8 KB | Display | |
Data in XML | emd_23390_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_23390_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23390 | HTTPS FTP |
-Related structure data
Related structure data | 7ljcMC 7ljdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23390.map.gz / Format: CCP4 / Size: 22.2 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: 1.045 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 : LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with...
+Supramolecule #1: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with...
+Macromolecule #1: D(1A) dopamine receptor
+Macromolecule #2: Engineered human Gs alpha subunit
+Macromolecule #3: 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 #5: Nanoboy 35
+Macromolecule #6: (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
+Macromolecule #7: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methy...
+Macromolecule #8: CHOLESTEROL
+Macromolecule #9: PALMITIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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: 212256 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |