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- PDB-8iy6: ETB-Gi complex bound to Endotheline-1, focused on receptor -

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Basic information

Entry
Database: PDB / ID: 8iy6
TitleETB-Gi complex bound to Endotheline-1, focused on receptor
Components
  • Endothelin type B receptor
  • Endothelin-1
KeywordsPEPTIDE BINDING PROTEIN / Class A GPCR / Endothelin / Gi / Vasoactive peptide
Function / homology
Function and homology information


: / endothelin A receptor binding / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / semaphorin-plexin signaling pathway involved in axon guidance ...: / endothelin A receptor binding / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of artery morphogenesis / cellular response to mineralocorticoid stimulus / histamine secretion / neural crest cell fate commitment / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / sympathetic neuron axon guidance / positive regulation of sarcomere organization / noradrenergic neuron differentiation / leukocyte activation / body fluid secretion / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / rough endoplasmic reticulum lumen / positive regulation of renal sodium excretion / : / pharyngeal arch artery morphogenesis / regulation of D-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 / Weibel-Palade body / endothelin receptor signaling pathway / response to ozone / podocyte differentiation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / positive regulation of cation channel activity / axonogenesis involved in innervation / glomerular filtration / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / regulation of pH / positive regulation of smooth muscle contraction / basal part of cell / response to salt / positive regulation of hormone secretion / cellular response to toxic substance / positive regulation of urine volume / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / signal transduction involved in regulation of gene expression / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / superoxide anion generation / cellular response to glucocorticoid stimulus / cartilage development / middle ear morphogenesis / negative regulation of protein metabolic process / cellular response to fatty acid / nitric oxide transport / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy / negative regulation of smooth muscle cell apoptotic process / response to testosterone / response to dexamethasone / thyroid gland development / cAMP/PKA signal transduction / cellular response to interleukin-1 / membrane depolarization / negative regulation of blood coagulation / positive regulation of cell size / response to amino acid / canonical Wnt signaling pathway / regulation of vasoconstriction / positive regulation of heart rate / transport vesicle / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / response to muscle stretch / positive regulation of endothelial cell migration / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / response to amphetamine / positive regulation of mitotic nuclear division / positive regulation of calcium-mediated signaling / cellular response to calcium ion / positive regulation of DNA-binding transcription factor activity / Peptide ligand-binding receptors
Similarity search - Function
Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / Endothelin family / Endothelin family signature. / Endothelin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsSano, F.K. / Akasaka, H. / Shihoya, W. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: 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
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Endothelin type B receptor
L: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)69,9902
Polymers69,9902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Endothelin type B receptor


Mass: 67492.219 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) / Strain (production host): Sf9 cells
#2: Protein/peptide Endothelin-1 / Preproendothelin-1 / PPET1


Mass: 2497.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05305
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Endothelin-1, ETB, and Gi / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 10408

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260085 / Symmetry type: POINT
RefinementResolution: 3.13→3.13 Å / Cor.coef. Fo:Fc: 0.877 / SU B: 20.883 / SU ML: 0.372 / ESU R: 0.39
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.44265 --
obs0.44265 38845 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 84.927 Å2
Refinement stepCycle: 1 / Total: 2495
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032554
ELECTRON MICROSCOPYf_angle_d0.5283474
ELECTRON MICROSCOPYf_dihedral_angle_d4.413337
ELECTRON MICROSCOPYf_chiral_restr0.036418
ELECTRON MICROSCOPYf_plane_restr0.004416
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork-2854 -
obs--100 %

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