+Open data
-Basic information
Entry | Database: PDB / ID: 7wu9 | |||||||||||||||||||||
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Title | Cryo-EM structure of the human EP3-Gi signaling complex | |||||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / GPCR / signal transduction / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex ...negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / Regulation of insulin secretion / G protein-coupled receptor binding / adenylate cyclase-activating G protein-coupled receptor 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 / response to peptide hormone / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GDP binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / nuclear envelope / retina development in camera-type eye / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / midbody / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / inflammatory response / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / synapse / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / 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: 3.375 Å | |||||||||||||||||||||
Authors | Suno, R. / Sugita, Y. / Morimoto, K. / Iwasaki, K. / Kato, T. / Kobayashi, T. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: Cell Rep / Year: 2022 Title: Structural insights into the G protein selectivity revealed by the human EP3-G signaling complex. Authors: Ryoji Suno / Yukihiko Sugita / Kazushi Morimoto / Hiroko Takazaki / Hirokazu Tsujimoto / Mika Hirose / Chiyo Suno-Ikeda / Norimichi Nomura / Tomoya Hino / Asuka Inoue / Kenji Iwasaki / ...Authors: Ryoji Suno / Yukihiko Sugita / Kazushi Morimoto / Hiroko Takazaki / Hirokazu Tsujimoto / Mika Hirose / Chiyo Suno-Ikeda / Norimichi Nomura / Tomoya Hino / Asuka Inoue / Kenji Iwasaki / Takayuki Kato / So Iwata / Takuya Kobayashi / Abstract: Prostaglandin receptors have been implicated in a wide range of functions, including inflammation, immune response, reproduction, and cancer. Our group has previously determined the crystal structure ...Prostaglandin receptors have been implicated in a wide range of functions, including inflammation, immune response, reproduction, and cancer. Our group has previously determined the crystal structure of the active-like EP3 bound to its endogenous agonist, prostaglandin E. Here, we present the single-particle cryoelectron microscopy (cryo-EM) structure of the human EP3-G signaling complex at a resolution of 3.4 Å. The structure reveals the binding mode of G to EP3 and the structural changes induced in EP3 by G binding. In addition, we compare the structure of the EP3-G complex with other subtypes of prostaglandin receptors (EP2 and EP4) bound to G that have been previously reported and examine the differences in amino acid composition at the receptor-G protein interface. Mutational analysis reveals that the selectivity of the G protein depends on specific amino acid residues in the second intracellular loop and TM5. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wu9.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wu9.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wu9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7wu9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7wu9_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 7wu9_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wu9 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wu9 | HTTPS FTP |
-Related structure data
Related structure data | 32824MC 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: 36175.887 Da / Num. of mol.: 1 / Mutation: A173I,V185S,N217Q,S258D,C289L,N308Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGER3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43115 |
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#2: Protein | Mass: 40427.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096 |
#3: Protein | Mass: 37728.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873 |
#4: 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768 |
#5: Antibody | Mass: 27318.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus agri (bacteria) |
-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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 10 mg/ml / 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 / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 0.07 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.375 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125572 / Symmetry type: POINT |