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- EMDB-35815: ETB-Gi complex bound to Endotheline-1, focused on receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-35815
TitleETB-Gi complex bound to Endotheline-1, focused on receptor
Map data
Sample
  • Complex: Complex of Endothelin-1, ETB, and Gi
    • Protein or peptide: Endothelin type B receptor
    • Protein or peptide: Endothelin-1
KeywordsClass A GPCR / Endothelin / Gi / Vasoactive peptide / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / positive regulation of artery morphogenesis ...positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / positive regulation of artery morphogenesis / semaphorin-plexin signaling pathway involved in axon guidance / body fluid 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 / positive regulation of renal sodium excretion / histamine secretion / leukocyte activation / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / regulation of D-glucose transmembrane transport / positive regulation of odontogenesis / epithelial fluid transport / endothelin receptor signaling pathway involved in heart process / negative regulation of hormone secretion / cardiac neural crest cell migration involved in outflow tract morphogenesis / Weibel-Palade body / response to leptin / endothelin receptor signaling pathway / response to ozone / podocyte differentiation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / artery smooth muscle contraction / glomerular filtration / axonogenesis involved in innervation / positive regulation of cation channel activity / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / regulation of pH / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / basal part of cell / cellular response to mineralocorticoid stimulus / positive regulation of smooth muscle contraction / response to salt / positive regulation of urine volume / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / negative regulation of blood coagulation / : / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / superoxide anion generation / positive regulation of neutrophil chemotaxis / positive regulation of signaling receptor activity / cartilage development / middle ear morphogenesis / cellular response to glucocorticoid stimulus / negative regulation of protein metabolic process / prostaglandin biosynthetic process / cellular response to fatty acid / nitric oxide transport / positive regulation of heart rate / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy / response to dexamethasone / response to testosterone / negative regulation of smooth muscle cell apoptotic process / thyroid gland development / membrane depolarization / positive regulation of cell size / cellular response to interleukin-1 / regulation of vasoconstriction / response to amino acid / canonical Wnt signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of JUN kinase activity / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / transport vesicle / protein kinase A signaling / response to muscle stretch / response to amphetamine / ERK1 and ERK2 cascade / positive regulation of calcium-mediated signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of mitotic nuclear division / cellular response to calcium ion
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsSano FK / Akasaka H / Shihoya W / Nureki O
Funding support Japan, 1 items
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, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35815.png

Downloads & links

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Map

FileDownload / File: emd_35815.map.gz / Format: CCP4 / Size: 1.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 86 pix.
= 99.932 Å		1.16 Å/pix.
x 68 pix.
= 79.016 Å		1.16 Å/pix.
x 80 pix.
= 92.96 Å

Surface

Projections

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.162 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.12
Minimum - Maximum-6.088579 - 6.920754
Average (Standard dev.)-0.041043565 (±0.43348587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin636137
Dimensions688086
Spacing806886
CellA: 92.95999 Å / B: 79.016 Å / C: 99.93199 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35815_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_35815_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35815_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex of Endothelin-1, ETB, and Gi

EntireName: Complex of Endothelin-1, ETB, and Gi
Components
  • Complex: Complex of Endothelin-1, ETB, and Gi
    • Protein or peptide: Endothelin type B receptor
    • Protein or peptide: Endothelin-1

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Supramolecule #1: Complex of Endothelin-1, ETB, and Gi

SupramoleculeName: Complex of Endothelin-1, ETB, and Gi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endothelin type B receptor

MacromoleculeName: Endothelin type B receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.492219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EERGFPPDRA TPLLQTAEIM TPPTKTLWPK GDYKDDDDKL APAEVPKGDR TAGSPPRTIS PPPCQGPIEI KETFKYINTV VSCLVFVLG IIGNSTLLRI IYKNKCMRNG PNILIASLAL GDLLHIVIDI PINVYKLLAE DWPFGAEMCK LVPFIQKASV G ITVLSLCA ...String:
EERGFPPDRA TPLLQTAEIM TPPTKTLWPK GDYKDDDDKL APAEVPKGDR TAGSPPRTIS PPPCQGPIEI KETFKYINTV VSCLVFVLG IIGNSTLLRI IYKNKCMRNG PNILIASLAL GDLLHIVIDI PINVYKLLAE DWPFGAEMCK LVPFIQKASV G ITVLSLCA LSIDRYRAVA SWSRIKGIGV PKWTAVEIVL IWVVSVVLAV PEAIGFDIIT MDYKGSYLRI CLLHPVQKTA FM QFYKTAK DWWLFSFYFC LPLAITAFFY TLMTCEMLRK KSGMQIALND HLKQRREVAK TVFCLVLVFA LCWLPLHLSR ILK LTLYNQ NDPNRCELLS FLLVLDYIGI NMASLNSCIN PIALYLVSKR FKNCFKSCLC CWCQSFEEKQ SLEEKQSCLK FKAN DHGYD NFRSSNKYSS SGSGGGGSGG SSSGGVFTLE DFVGDWEQTA AYNLDQVLEQ GGVSSLLQNL AVSVTPIQRI VRSGE NALK IDIHVIIPYE GLSADQMAQI EEVFKVVYPV DDHHFKVILP YGTLVIDGVT PNMLNYFGRP YEGIAVFDGK KITVTG TLW NGNKIIDERL ITPDGSMLFR VTINSGGSGG GGSGGSSSGG LEVLFQ

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Macromolecule #2: Endothelin-1

MacromoleculeName: Endothelin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.497951 KDa
SequenceString:
CSCSSLMDKE CVYFCHLDII W

UniProtKB: Endothelin-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 10408 / Average exposure time: 2.3 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260085
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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