+Open data
-Basic information
Entry | Database: PDB / ID: 7wy5 | ||||||
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Title | ADGRL3/Gq complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / GPCR | ||||||
Function / homology | Function and homology information locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / synapse organization / neuron migration ...locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / synapse organization / neuron migration / Olfactory Signaling Pathway / Schaffer collateral - CA1 synapse / 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 / 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 / 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 / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell junction / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / carbohydrate binding / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / axon / GTPase activity / glutamatergic synapse / calcium ion binding / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||
Authors | He, Y. / Qian, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural insights into adhesion GPCR ADGRL3 activation and G, G, G, and G coupling. Authors: Yu Qian / Zhengxiong Ma / Chunhong Liu / Xinzhi Li / Xinyan Zhu / Na Wang / Zhenmei Xu / Ruixue Xia / Jiale Liang / Yaning Duan / Han Yin / Yangjie Xiong / Anqi Zhang / Changyou Guo / Zheng ...Authors: Yu Qian / Zhengxiong Ma / Chunhong Liu / Xinzhi Li / Xinyan Zhu / Na Wang / Zhenmei Xu / Ruixue Xia / Jiale Liang / Yaning Duan / Han Yin / Yangjie Xiong / Anqi Zhang / Changyou Guo / Zheng Chen / Zhiwei Huang / Yuanzheng He / Abstract: Adhesion G-protein-coupled receptors (aGPCRs) play key roles in a diversity of physiologies. A hallmark of aGPCR activation is the removal of the inhibitory GAIN domain and the dipping of the cleaved ...Adhesion G-protein-coupled receptors (aGPCRs) play key roles in a diversity of physiologies. A hallmark of aGPCR activation is the removal of the inhibitory GAIN domain and the dipping of the cleaved stalk peptide into the ligand-binding pocket of receptors; however, the detailed mechanism remains obscure. Here, we present cryoelectron microscopy (cryo-EM) structures of ADGRL3 in complex with G, G, G, and G. The structures reveal unique ligand-engaging mode, distinctive activation conformation, and key mechanisms of aGPCR activation. The structures also reveal the uncharted structural information of GPCR/G coupling. A comparison of G, G, G, and G engagements with ADGRL3 reveals the key determinant of G-protein coupling on the far end of αH5 of Gα. A detailed analysis of the engagements allows us to design mutations that specifically enhance one pathway over others. Taken together, our study lays the groundwork for understanding aGPCR activation and G-protein-coupling selectivity. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wy5.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wy5.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wy5_validation.pdf.gz | 694.9 KB | Display | wwPDB validaton report |
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Full document | 7wy5_full_validation.pdf.gz | 694.6 KB | Display | |
Data in XML | 7wy5_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 7wy5_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/7wy5 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/7wy5 | HTTPS FTP |
-Related structure data
Related structure data | 32884MC 7wy8C 7wybC 7x10C 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: 41855.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Insect BA phytoplasma (bacteria) |
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#2: Protein | Mass: 37915.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Insect BA phytoplasma (bacteria) / References: UniProt: P62873 |
#3: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Insect BA phytoplasma (bacteria) / References: UniProt: P59768 |
#4: Protein | Mass: 17381.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Insect BA phytoplasma (bacteria) |
#5: Protein | Mass: 172044.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrl3, Kiaa0768, Lec3, Lphn3 / Production host: Insect BA phytoplasma (bacteria) / References: UniProt: Q80TS3 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GPCR/G-protein complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Insect BA phytoplasma (bacteria) |
Buffer solution | pH: 7.5 |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM diffraction | Camera length: 800 mm |
EM diffraction shell | Resolution: 3→5.5 Å / Fourier space coverage: 93.2 % / Multiplicity: 2.5 / Num. of structure factors: 244 / Phase residual: 13.5 ° |
EM diffraction stats | Fourier space coverage: 90.3 % / High resolution: 2.83 Å / Num. of intensities measured: 1590 / Num. of structure factors: 325 / Phase error rejection criteria: 20 / Rmerge: 0.198 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370000 / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||
Atomic model building | PDB-ID: 6VMS Pdb chain-ID: A |