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Yorodumi- PDB-7ljc: Allosteric modulator LY3154207 binding to SKF-81297-bound dopamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ljc | |||||||||||||||
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Title | Allosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Dopamine receptor 2 / Gs protein / SKF-81297 / PAM / LY3154207 | |||||||||||||||
Function / homology | Function and homology information dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / operant conditioning / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / dopamine binding / heterotrimeric G-protein binding / peristalsis ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / operant conditioning / regulation of dopamine uptake involved in synaptic transmission / modification of postsynaptic structure / dopamine binding / heterotrimeric G-protein binding / peristalsis / regulation of dopamine metabolic process / G protein-coupled receptor complex / sensitization / phospholipase C-activating dopamine receptor signaling pathway / grooming behavior / dopamine transport / positive regulation of neuron migration / habituation / astrocyte development / positive regulation of potassium ion transport / striatum development / conditioned taste aversion / 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 / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / arrestin family protein binding / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / non-motile cilium / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / adult walking behavior / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (i) signalling events / 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 / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / alkylglycerophosphoethanolamine phosphodiesterase activity / long-term synaptic depression / mating behavior / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / 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 / dopamine metabolic process / transmission of nerve impulse / glucose import / PKA activation in glucagon signalling / behavioral response to cocaine / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / hair follicle placode formation / neuronal action potential / photoreceptor outer segment / developmental growth / G-protein alpha-subunit binding / D1 dopamine receptor binding / intracellular transport / GABA-ergic synapse / behavioral fear response / Hedgehog 'off' state / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / cardiac muscle cell apoptotic process Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) Bos taurus (cattle) Lama glama (llama) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||
Authors | Zhuang, Y. / Krumm, B. / Zhang, H. / Zhou, X.E. / Wang, Y. / Guo, J. / Huang, X.-P. / Liu, Y. / Wang, L. / Cheng, X. ...Zhuang, Y. / Krumm, B. / Zhang, H. / Zhou, X.E. / Wang, Y. / Guo, J. / Huang, X.-P. / Liu, Y. / Wang, L. / Cheng, X. / Jiang, Y. / Jiang, H. / Melcher, K. / Zhang, C. / Yi, W. / Roth, B.L. / Zhang, Y. / Xu, H.E. | |||||||||||||||
Funding support | China, United States, 4items
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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, X.E. / Wang, Y. / Guo, J. / Huang, X.-P. / Liu, Y. / Wang, L. / Cheng, X. / Jiang, Y. / Jiang, H. / Melcher, K. / Zhang, C. / Yi, W. / Roth, B.L. / Zhang, Y. / Xu, H.E. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ljc.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ljc.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ljc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ljc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ljc_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ljc_validation.xml.gz | 34 KB | Display | |
Data in CIF | 7ljc_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/7ljc ftp://data.pdbj.org/pub/pdb/validation_reports/lj/7ljc | HTTPS FTP |
-Related structure data
Related structure data | 23390MC 7ljdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules RA
#1: Protein | Mass: 55668.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DRD1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21728 |
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#2: Protein | Mass: 29048.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63092*PLUS |
-Guanine nucleotide-binding protein ... , 2 types, 2 molecules BG
#3: Protein | Mass: 39020.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54311 |
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#4: Protein | Mass: 7432.554 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212 |
-Antibody , 1 types, 1 molecules N
#5: Antibody | Mass: 14845.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 14 molecules
#6: Chemical | ChemComp-SK0 / ( | ||
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#7: Chemical | ChemComp-G4C / | ||
#8: Chemical | ChemComp-CLR / #9: Chemical | ChemComp-PLM / |
-Details
Has ligand of interest | Y |
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-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: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with Gi protein Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||
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 |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212256 / Symmetry type: POINT |