+Open data
-Basic information
Entry | Database: PDB / ID: 8iy5 | ||||||
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Title | ETB-Gi complex bound to endothelin-1 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Class A GPCR / Endothelin / Gi / Vasoactive peptide | ||||||
Function / homology | Function and homology information positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment ...positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment / sympathetic neuron axon guidance / positive regulation of artery morphogenesis / body fluid secretion / glomerular endothelium development / vein smooth muscle contraction / noradrenergic neuron differentiation / response to prostaglandin F / positive regulation of renal sodium excretion / positive regulation of sarcomere organization / leukocyte activation / histamine secretion / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / regulation of glucose transmembrane transport / positive regulation of odontogenesis / endothelin receptor signaling pathway involved in heart process / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / endothelin receptor signaling pathway / response to ozone / Weibel-Palade body / podocyte differentiation / renal sodium ion absorption / glomerular filtration / positive regulation of cell growth involved in cardiac muscle cell development / artery smooth muscle contraction / axonogenesis involved in innervation / positive regulation of cation channel activity / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / positive regulation of urine volume / basal part of cell / respiratory gaseous exchange by respiratory system / positive regulation of smooth muscle contraction / response to salt / regulation of pH / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / protein kinase C-activating G protein-coupled receptor signaling pathway / embryonic heart tube development / negative regulation of blood coagulation / dorsal/ventral pattern formation / superoxide anion generation / axon extension / positive regulation of neutrophil chemotaxis / middle ear morphogenesis / positive regulation of signaling receptor activity / cartilage development / cellular response to glucocorticoid stimulus / 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 / 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 / prostaglandin biosynthetic process / G alpha (q) signalling events / negative regulation of protein metabolic process / nitric oxide transport / cellular response to fatty acid / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / branching involved in blood vessel morphogenesis / positive regulation of heart rate / Vasopressin regulates renal water homeostasis via Aquaporins / : Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus rattus (black rat) Bos taurus (cattle) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Sano, F.K. / Akasaka, H. / Shihoya, W. / Nureki, O. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Elife / Year: 2023 Title: Cryo-EM structure of the endothelin-1-ET-G complex. Authors: Fumiya K Sano / Hiroaki Akasaka / Wataru Shihoya / Osamu Nureki / Abstract: The endothelin ET receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ET signaling induces reactive astrocytes in the brain and vasorelaxation in ...The endothelin ET receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ET signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ET agonists are expected to be drugs for neuroprotection and improved anti-tumor drug delivery. Here, we report the cryo-electron microscopy structure of the endothelin-1-ET-G complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ET receptor structures revealed how endothelin-1 activates the ET receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ET, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ET binds G in the shallowest position, further expanding the diversity of G-protein binding modes. This structural information will facilitate the elucidation of G-protein activation and the rational design of ET agonists. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iy5.cif.gz | 244.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iy5.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 8iy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iy5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8iy5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8iy5_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 8iy5_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iy5 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iy5 | HTTPS FTP |
-Related structure data
Related structure data | 35814MC 8iy6C 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
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 40415.031 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) / Strain (production host): sf9 cells / References: UniProt: P63096 |
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#2: Protein | Mass: 40470.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 cells |
#3: Protein | Mass: 7563.750 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) / Strain (production host): sf9 cells / References: UniProt: P63212 |
-Antibody / Protein / Protein/peptide , 3 types, 3 molecules ERL
#4: Antibody | Mass: 27720.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 cells |
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#5: Protein | Mass: 67492.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) |
#6: Protein/peptide | Mass: 2497.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05305 |
-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: Complex of Endothelin-1, ETB, Gi trimer and scFv16 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 2.3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 10408 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260085 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Resolution: 2.8→148.74 Å / Cor.coef. Fo:Fc: 0.817 / SU B: 14.414 / SU ML: 0.28 / ESU R: 0.338 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.348 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 9077 | ||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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