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- EMDB-38740: Cryo-EM structure of ET-1 bound ETBR-DNGI complex -

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Entry
Database: EMDB / ID: EMD-38740
TitleCryo-EM structure of ET-1 bound ETBR-DNGI complex
Map data
Sample
  • Complex: ET-1 BOUND ETBR-GI COMPLEX
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: SCFV16
KeywordsENDOTHELIN / RECEPTOR / Gi / COMPLEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / negative regulation of phospholipase C/protein kinase C signal transduction / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin receptor activity ...enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / negative regulation of phospholipase C/protein kinase C signal transduction / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin receptor activity / peptide hormone secretion / endothelin B receptor binding / aldosterone metabolic process / 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 / regulation of fever generation / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / positive regulation of penile erection / sympathetic neuron axon guidance / positive regulation of sarcomere organization / noradrenergic neuron differentiation / leukocyte activation / positive regulation of chemokine-mediated signaling pathway / body fluid secretion / maternal process involved in parturition / rough endoplasmic reticulum lumen / neuroblast migration / heparin proteoglycan metabolic process / positive regulation of renal sodium excretion / posterior midgut development / 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 / : / developmental pigmentation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / response to sodium phosphate / renal sodium excretion / enteric nervous system development / positive regulation of cation channel activity / axonogenesis involved in innervation / glomerular filtration / protein transmembrane transport / renin secretion into blood stream / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / renal albumin absorption / melanocyte differentiation / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / regulation of pH / positive regulation of smooth muscle contraction / basal part of cell / peripheral nervous system development / response to salt / positive regulation of hormone secretion / type 1 angiotensin receptor binding / cellular response to toxic substance / positive regulation of urine volume / negative regulation of adenylate cyclase activity / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / regulation of epithelial cell proliferation / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / establishment of endothelial barrier / signal transduction involved in regulation of gene expression / neural crest cell migration / 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 / cGMP-mediated signaling / cellular response to fatty acid / nitric oxide transport / response to pain / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / G-protein alpha subunit, group I ...Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endothelin-1 / Endothelin receptor type B / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsTani K / Maki-Yonekura S / Kanno R / Negami T / Hamaguchi T / Hall M / Mizoguchi A / Humbel BM / Terada T / Yonekura K / Doi T
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121004 Japan
Japan Society for the Promotion of Science (JSPS)20H03210 Japan
CitationJournal: Commun Biol / Year: 2024
Title: Structure of endothelin ET receptor-G complex in a conformation stabilized by unique NPxxL motif.
Authors: Kazutoshi Tani / Saori Maki-Yonekura / Ryo Kanno / Tatsuki Negami / Tasuku Hamaguchi / Malgorzata Hall / Akira Mizoguchi / Bruno M Humbel / Tohru Terada / Koji Yonekura / Tomoko Doi /
Abstract: Endothelin type B receptor (ETR) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ETR activation by the ...Endothelin type B receptor (ETR) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ETR activation by the endogenous peptide hormones endothelin (ET)-1-3 stimulates several signaling pathways, including G, G, G, G, and β-arrestin. Although the conserved NPxxY motif in transmembrane helix 7 (TM7) is important during GPCR activation, ETR possesses the lesser known NPxxL motif. In this study, we present the cryo-EM structure of the ETR-G complex, complemented by MD simulations and functional studies. These investigations reveal an unusual movement of TM7 to the intracellular side during ETR activation and the essential roles of the diverse NPxxL motif in stabilizing the active conformation of ETR and organizing the assembly of the binding pocket for the α5 helix of G protein. These findings enhance our understanding of the interactions between GPCRs and G proteins, thereby advancing the development of therapeutic strategies.
History
DepositionJan 16, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38740.png

Downloads & links

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Map

FileDownload / File: emd_38740.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 192 pix.
= 228.48 Å		1.19 Å/pix.
x 192 pix.
= 228.48 Å		1.19 Å/pix.
x 192 pix.
= 228.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.148493 - 0.21696313
Average (Standard dev.)0.000054176497 (±0.004675841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 228.48001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38740_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_38740_half_map_2.map
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Sample components

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Entire : ET-1 BOUND ETBR-GI COMPLEX

EntireName: ET-1 BOUND ETBR-GI COMPLEX
Components
  • Complex: ET-1 BOUND ETBR-GI COMPLEX
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: SCFV16

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Supramolecule #1: ET-1 BOUND ETBR-GI COMPLEX

SupramoleculeName: ET-1 BOUND ETBR-GI COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endothelin receptor type B

MacromoleculeName: Endothelin receptor type B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.808262 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PGGGLAPAEV PKGDRTAGSP PRTISPPPCQ GPIEIKETFK YINTVVSCLV FVLGIIGNST LLYIIYKNKC MRNGPNILIA SLALGDLLH IVIDIPINVY KLLAEDWPFG AEMCKLVPFI QKASVGITVL SLCALSIDRY RAVASWSRIK GIGVPKWTAV E IVLIWVVS ...String:
PGGGLAPAEV PKGDRTAGSP PRTISPPPCQ GPIEIKETFK YINTVVSCLV FVLGIIGNST LLYIIYKNKC MRNGPNILIA SLALGDLLH IVIDIPINVY KLLAEDWPFG AEMCKLVPFI QKASVGITVL SLCALSIDRY RAVASWSRIK GIGVPKWTAV E IVLIWVVS VVLAVPEAIG FDIITMDYKG SYLRICLLHP VQKTAFMQFY KTAKDWWLFS FYFCLPLAIT AFFYTLMTCE ML RKKSGMQ IALNDHLKQR REVAKTVFCL VLVFALCWLP LHLSRILKLT LYNQNDPNRC ELLSFLLVLD YIGINMASLN SCI NPIALY LVSKRFKNAF KSALCCWAQS

UniProtKB: Endothelin receptor type B

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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
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
CSCSSLMDKE CVYFCHLDII W

UniProtKB: Endothelin-1

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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.414047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.671102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PGSSGSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
PGSSGSELDQ 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 DSFLKIWN

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

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Macromolecule #5: 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
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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

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Macromolecule #6: SCFV16

MacromoleculeName: SCFV16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.39893 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFT ISRDDPKNTL FLQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV M TQATSSVP ...String:
MVSAIVLYVL LAAAAHSAFA DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFT ISRDDPKNTL FLQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV M TQATSSVP VTPGESVSIS CRSSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LE AEDVGVY YCMQHLEYPL TFGAGTKLEL KGSLEVLFQG

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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

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1038215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8xwp:
Cryo-EM structure of ET-1 bound ETBR-DNGI complex

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