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- EMDB-38702: Cryo-EM structure of ETBR bound with BQ3020 -

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Basic information

Entry
Database: EMDB / ID: EMD-38702
TitleCryo-EM structure of ETBR bound with BQ3020
Map data
Sample
  • Complex: Complex of protein Gsq with ETB and BQ3020
    • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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: Nanobody 35
    • Protein or peptide: BQ3020
    • Protein or peptide: Exo-alpha-sialidase,Endothelin receptor type B
KeywordsGPCR / COMPLEX / ETB / BQ3020 / SIGNALING PROTEIN
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / aldosterone metabolic process / negative regulation of neuron maturation / chordate pharynx development / endothelin receptor activity / regulation of fever generation / vein smooth muscle contraction / positive regulation of penile erection / neuroblast migration ...enteric smooth muscle cell differentiation / response to endothelin / aldosterone metabolic process / negative regulation of neuron maturation / chordate pharynx development / endothelin receptor activity / regulation of fever generation / vein smooth muscle contraction / positive regulation of penile erection / neuroblast migration / heparin metabolic process / posterior midgut development / epithelial fluid transport / endothelin receptor signaling pathway / podocyte differentiation / developmental pigmentation / renal sodium ion absorption / response to sodium phosphate / renal sodium excretion / protein transmembrane transport / enteric nervous system development / renin secretion into blood stream / melanocyte differentiation / regulation of pH / renal albumin absorption / positive regulation of urine volume / peripheral nervous system development / negative regulation of adenylate cyclase activity / vasoconstriction / regulation of epithelial cell proliferation / type 1 angiotensin receptor binding / establishment of endothelial barrier / negative regulation of protein metabolic process / neural crest cell migration / cGMP-mediated signaling / response to pain / : / : / : / exo-alpha-sialidase / macrophage chemotaxis / peptide hormone binding / canonical Wnt signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of heart rate / Peptide ligand-binding receptors / calcium-mediated signaling / calcium ion transmembrane transport / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / response to organic cyclic compound / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / vasodilation / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / nervous system development / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / gene expression / fibroblast proliferation / G alpha (i) signalling events / G alpha (s) signalling events / cellular response to lipopolysaccharide / nuclear membrane
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / : / BNR repeat-like domain / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily ...Endothelin receptor B / Endothelin receptor family / : / BNR repeat-like domain / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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 / exo-alpha-sialidase
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHou JY / Liu SH / Wu LJ / Liu ZJ / Hua T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2024
Title: Structural basis of antagonist selectivity in endothelin receptors.
Authors: Junyi Hou / Shenhui Liu / Xiaodan Zhang / Guowei Tu / Lijie Wu / Yijie Zhang / Hao Yang / Xiangcheng Li / Junlin Liu / Longquan Jiang / Qiwen Tan / Fang Bai / Zhijie Liu / Changhong Miao / Tian Hua / Zhe Luo /
Abstract: Endothelins and their receptors, ET and ET, play vital roles in maintaining vascular homeostasis. Therapeutically targeting endothelin receptors, particularly through ET antagonists, has shown ...Endothelins and their receptors, ET and ET, play vital roles in maintaining vascular homeostasis. Therapeutically targeting endothelin receptors, particularly through ET antagonists, has shown efficacy in treating pulmonary arterial hypertension (PAH) and other cardiovascular- and renal-related diseases. Here we present cryo-electron microscopy structures of ET in complex with two PAH drugs, macitentan and ambrisentan, along with zibotentan, a selective ET antagonist, respectively. Notably, a specialized anti-ET antibody facilitated the structural elucidation. These structures, together with the active-state structures of ET-1-bound ET and ET, and the agonist BQ3020-bound ET, in complex with G, unveil the molecular basis of agonist/antagonist binding modes in endothelin receptors. Key residues that confer antagonist selectivity to endothelin receptors were identified along with the activation mechanism of ET. Furthermore, our results suggest that ECL2 in ET can serve as an epitope for antibody-mediated receptor antagonism. Collectively, these insights establish a robust theoretical framework for the rational design of small-molecule drugs and antibodies with selective activity against endothelin receptors.
History
DepositionJan 15, 2024-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38702.png

Downloads & links

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Map

FileDownload / File: emd_38702.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017709819 - 1.8785503
Average (Standard dev.)0.00093805353 (±0.022419663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of protein Gsq with ETB and BQ3020

EntireName: Complex of protein Gsq with ETB and BQ3020
Components
  • Complex: Complex of protein Gsq with ETB and BQ3020
    • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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: Nanobody 35
    • Protein or peptide: BQ3020
    • Protein or peptide: Exo-alpha-sialidase,Endothelin receptor type B

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Supramolecule #1: Complex of protein Gsq with ETB and BQ3020

SupramoleculeName: Complex of protein Gsq with ETB and BQ3020 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit...

MacromoleculeName: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.464314 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHENLY FQGNSKTEDQ RNEEKAQREA NKKIEKQLQK DKQVYRATHR LLLLGADNSG KSTIVKQMRI LHGGSGGSGG TSGIFETKF QVDKVNFHMF DVGGQRDERR KWIQCFNDVT AIIFVVDSSD YNRLQEALNL FKSIWNNRWL RTISVILFLN K QDLLAEKV ...String:
HHHHHHENLY FQGNSKTEDQ RNEEKAQREA NKKIEKQLQK DKQVYRATHR LLLLGADNSG KSTIVKQMRI LHGGSGGSGG TSGIFETKF QVDKVNFHMF DVGGQRDERR KWIQCFNDVT AIIFVVDSSD YNRLQEALNL FKSIWNNRWL RTISVILFLN K QDLLAEKV LAGKSKIEDY FPEFARYTTP EDATPEPGED PRVTRAKYFI RDEFLRISTA SGDGRHYCYP HFTCAVDTEN AR RIFNDCK DIILQMNLRE YNLV

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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: Homo sapiens (human)
Molecular weightTheoretical: 38.045629 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: IGRARGFSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG ...String:
IGRARGFSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CF FPNGNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADRAGVLAGH DNR VSCLGV TDDGMAVATG SWDSFLKIWN

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

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Macromolecule #3: 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: 3 / 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 #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 17.057271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV SSHHHHHH

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Macromolecule #5: BQ3020

MacromoleculeName: BQ3020 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.966302 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LMDKEAVYFA HLDIIW

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Macromolecule #6: Exo-alpha-sialidase,Endothelin receptor type B

MacromoleculeName: Exo-alpha-sialidase,Endothelin receptor type B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.123805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAGRAVEG AVKTEPVDLF HPGFLNSSNY RIPALFKTKE GTLIASIDAR RHGGADAPNN DIDTAVRRS EDGGKTWDEG QIIMDYPDKS SVIDTTLIQD DETGRIFLLV THFPSKYGFW NAGLGSGFKN IDGKEYLCLY D SSGKEFTV ...String:
MKTIIALSYI FCLVFADYKD DDDAGRAVEG AVKTEPVDLF HPGFLNSSNY RIPALFKTKE GTLIASIDAR RHGGADAPNN DIDTAVRRS EDGGKTWDEG QIIMDYPDKS SVIDTTLIQD DETGRIFLLV THFPSKYGFW NAGLGSGFKN IDGKEYLCLY D SSGKEFTV RENVVYDKDS NKTEYTTNAL GDLFKNGTKI DNINSSTAPL KAKGTSYINL VYSDDDGKTW SEPQNINFQV KK DWMKFLG IAPGRGIQIK NGEHKGRIVV PVYYTNEKGK QSSAVIYSDD SGKNWTIGES PNDNRKLENG KIINSKTLSD DAP QLTECQ VVEMPNGQLK LFMRNLSGYL NIATSFDGGA TWDETVEKDT NVLEPYCQLS VINYSQKVDG KDAVIFSNPN ARSR SNGTV RIGLINQVGT YENGEPKYEF DWKYNKLVKP GYYAYSCLTE LSNGNIGLLY EGTPSEEMSY IEMNLKYLES GANKA PAEV PKGDRTAGSP PRTISPPPCQ GPIEIKETFK YINTVVSCLV FVLGIIGNST LLRIIYKNKC MRNGPNILIA SLALGD LLH IVIDIPINVY KLLAEDWPFG AEMCKLVPFI QKASVGITVL SLCALSIDRY RAVASWSRIK GIGVPKWTAV EIVLIWV VS VVLAVPEAIG FDIITMDYKG SYLRICLLHP VQKTAFMQFY KTAKDWWLFS FYFCLPLAIT AFFYTLMTCE MLRKKSGM Q IALNDHLKQR REVAKTVFCL VLVFALCWLP LHLSRILKLT LYNQNDPNRC ELLSFLLVLD YIGINMASLN SCINPIALY LVSKRFKNCF KSCLCCWCQL EVLFQGPHHH HHHHHHH

UniProtKB: exo-alpha-sialidase, Endothelin receptor type B

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118372
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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