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- PDB-7joz: Crystal structure of dopamine D1 receptor in complex with G prote... -
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Basic information
Entry | Database: PDB / ID: 7joz | ||||||
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Title | Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist | ||||||
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![]() | MEMBRANE PROTEIN / Dopamine receptor / D1 / non-catechol agonist / G protein | ||||||
Function / homology | ![]() dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / operant conditioning / dopamine neurotransmitter receptor activity, coupled via Gs / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / heterotrimeric G-protein binding / regulation of dopamine metabolic process ...dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / operant conditioning / dopamine neurotransmitter receptor activity, coupled via Gs / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / heterotrimeric G-protein binding / regulation of dopamine metabolic process / sensitization / peristalsis / G protein-coupled receptor complex / dopamine transport / phospholipase C-activating dopamine receptor signaling pathway / grooming behavior / positive regulation of neuron migration / habituation / astrocyte development / conditioned taste aversion / positive regulation of potassium ion transport / striatum development / dentate gyrus development / maternal behavior / arrestin family protein binding / non-motile cilium / adult walking behavior / mating behavior / long-term synaptic depression / ciliary membrane / G protein-coupled dopamine receptor signaling pathway / temperature homeostasis / dopamine metabolic process / transmission of nerve impulse / glucose import / PKA activation in glucagon signalling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral response to cocaine / hair follicle placode formation / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / G-protein alpha-subunit binding / intracellular transport / GABA-ergic synapse / D1 dopamine receptor binding / neuronal action potential / behavioral fear response / Hedgehog 'off' state / prepulse inhibition / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / viral release from host cell by cytolysis / synapse assembly / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / presynaptic modulation of chemical synaptic transmission / peptidoglycan catabolic process / positive regulation of synaptic transmission, glutamatergic / positive regulation of release of sequestered calcium ion into cytosol / trans-Golgi network membrane / synaptic transmission, glutamatergic / G protein-coupled receptor activity / long-term synaptic potentiation / regulation of protein phosphorylation / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / visual learning / Activation of the phototransduction cascade / bone development / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / memory / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / cognition / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / cilium / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / platelet aggregation / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, B. / Feng, D. / Chu, M.L. / Fish, I. / Kelm, S. / Lebon, F. / Lovera, S. / Valade, A. / Wood, M. / Ceska, T. ...Sun, B. / Feng, D. / Chu, M.L. / Fish, I. / Kelm, S. / Lebon, F. / Lovera, S. / Valade, A. / Wood, M. / Ceska, T. / Kobilka, T.S. / Sands, Z. / Kobilka, B.K. | ||||||
![]() | ![]() Title: Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist. Authors: Sun, B. / Feng, D. / Chu, M.L. / Fish, I. / Lovera, S. / Sands, Z.A. / Kelm, S. / Valade, A. / Wood, M. / Ceska, T. / Kobilka, T.S. / Lebon, F. / Kobilka, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 557 KB | Display | ![]() |
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PDB format | ![]() | 400.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 714 KB | Display | ![]() |
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Full document | ![]() | 726.7 KB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sn6S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG
#1: Protein | Mass: 44326.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 38534.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody / Protein , 2 types, 2 molecules NR
#4: Antibody | Mass: 17352.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#5: Protein | Mass: 59856.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: e, T4Tp126, DRD1 / Production host: ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/VFP.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/1PE.gif)
#6: Chemical | ChemComp-VFP / |
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#7: Chemical | ChemComp-1PE / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 65.6 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 0.1M MES pH 6.5, 0.1M Ammonium Dibasic Citrate, 18-25% (w/w) PEG400, 1mM TCEP, 10uM UCB1575401 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.79→49 Å / Num. obs: 20110 / % possible obs: 94.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 127.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.116 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.79→4.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.904 / Num. unique obs: 4783 / CC1/2: 0.468 / Rpim(I) all: 0.555 / % possible all: 95.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3SN6 Resolution: 3.8→47 Å / SU ML: 0.5539 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3177 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 139.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.32450069099 Å / Origin y: -38.0969843562 Å / Origin z: -40.5635125984 Å
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Refinement TLS group | Selection details: all |