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- EMDB-38330: ETB-eGt complex bound to endothelin-1 -

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Entry
Database: EMDB / ID: EMD-38330
TitleETB-eGt complex bound to endothelin-1
Map data
Sample
  • Complex: Complex of Endothelin-1, ETB, eGt trimer and Nb35*
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Camelid antibody VHH fragment
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,eGt-alpha
KeywordsSIGNALING PROTEIN / PEPTIDE BINDING PROTEIN-IMMUNE SYSTEM complex
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 / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / endothelin receptor signaling pathway / Weibel-Palade body / 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 / positive regulation of cation channel activity / axonogenesis involved in innervation / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / : / 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 / negative regulation of protein metabolic process / 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 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / prostaglandin biosynthetic process / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / cellular response to glucocorticoid stimulus / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / cellular response to fatty acid / nitric oxide transport / G alpha (q) signalling events / positive regulation of heart rate / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / branching involved in blood vessel morphogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of cardiac muscle hypertrophy
Similarity search - Function
Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / Endothelin family / Endothelin family signature. / Endothelin / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily ...Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / Endothelin family / Endothelin family signature. / Endothelin / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain
Similarity search - Domain/homology
Endothelin-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (cattle) / Rattus rattus (black rat) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOshima HS / Sano FK / Akasaka H / Iwama A / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Optimizing cryo-EM structural analysis of G-coupling receptors via engineered G and Nb35 application.
Authors: Hidetaka S Oshima / Fumiya K Sano / Hiroaki Akasaka / Aika Iwama / Wataru Shihoya / Osamu Nureki /
Abstract: Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in ...Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in the case of GPCR-G complexes, scFv16, an antibody that recognizes the intricate interface of the complex, has been mainly implemented to stabilize the complex. However, owing to their flexibility and heterogeneity, structural determinations of GPCR-G complexes remain both challenging and resource-intensive. By employing eGα, which exhibits binding affinity to modified nanobody Nb35, the cryo-EM structure of Rhodopsin-eGα complex was previously reported. Using this modified G protein, we determined the structure of the ET-eG complex bound to the modified Nb35. The determined structure of ET receptor was the same as the previously reported ET-G complex, and the resulting dataset demonstrated significantly improved anisotropy. This modified G protein will be utilized for the structural determination of other GPCR-G complexes.
History
DepositionDec 15, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38330.png

Downloads & links

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Map

FileDownload / File: emd_38330.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.97 Å/pix.
x 240 pix.
= 232.4 Å		0.97 Å/pix.
x 240 pix.
= 232.4 Å		0.97 Å/pix.
x 240 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-18.689352 - 35.821227999999998
Average (Standard dev.)0.0025409844 (±1.0766505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 232.39992 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38330_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_38330_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Endothelin-1, ETB, eGt trimer and Nb35*

EntireName: Complex of Endothelin-1, ETB, eGt trimer and Nb35*
Components
  • Complex: Complex of Endothelin-1, ETB, eGt trimer and Nb35*
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Camelid antibody VHH fragment
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,eGt-alpha

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Supramolecule #1: Complex of Endothelin-1, ETB, eGt trimer and Nb35*

SupramoleculeName: Complex of Endothelin-1, ETB, eGt trimer and Nb35* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4-#5, #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2...

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,eGt-alpha
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 48.998785 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGCTLSAED KAAVERSKMI DRNLREDGEK AARTVKLLLL GAGESGKSTI VKQMKIIHQD GYSLEECLEF IAIIYGNTLQ S ILAIVRAM ...String:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGCTLSAED KAAVERSKMI DRNLREDGEK AARTVKLLLL GAGESGKSTI VKQMKIIHQD GYSLEECLEF IAIIYGNTLQ S ILAIVRAM TTLNIQYGDS ARQDDARKLM HMADTIEEGT MPKEMSDIIQ RLWKDSGIQA CFDRASEYQL NDSAGYYLSD LE RLVTPGY VPTEQDVLRS RVKTTGIIET QFSFKDLNFR MFDVGGQRDE RRKWIHCFEG VTAIIFCVAL SDYDMVLVED NQT NRMQES MNLFKSICNN KWFTDTSIIL FLNKKDLFEE KIKKSPLTDY YPEYAGSNTY EEAGNYIKVQ FLELNMASDV KEIY SHMTC ATDTQNVKFV FDAVTDIIIK ENLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus rattus (black rat)
Molecular weightTheoretical: 40.470105 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWNGA SGGGSGGNSG SSGGSSGVSG WRLFKKIS

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Macromolecule #3: Camelid antibody VHH fragment

MacromoleculeName: Camelid antibody VHH fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 17.395631 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLQW VSDISQSGAS ISYTGSVKG RFTISRDDAK NTLYLQMNSL KPADTAVYYC ARCPAPFTRD CFDVTSTAYA YRGQGTQVTV SSHHHHHHEP E A

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Macromolecule #4: Endothelin receptor type B

MacromoleculeName: Endothelin receptor type B / type: protein_or_peptide / ID: 4 / 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 #5: Endothelin-1

MacromoleculeName: Endothelin-1 / type: protein_or_peptide / ID: 5 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52285
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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