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

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Basic information

Entry
Database: PDB / ID: 8xwp
TitleCryo-EM structure of ET-1 bound ETBR-DNGI complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Endothelin receptor type B
  • Endothelin-1
  • SCFV16
KeywordsMEMBRANE PROTEIN / ENDOTHELIN / RECEPTOR / Gi / COMPLEX
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / negative regulation of neuron maturation / endothelin A receptor binding / protein kinase C deactivation / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation ...enteric smooth muscle cell differentiation / response to endothelin / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / negative regulation of neuron maturation / endothelin A receptor binding / protein kinase C deactivation / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / endothelin receptor activity / peptide hormone secretion / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / positive regulation of artery morphogenesis / body fluid secretion / neural crest cell fate commitment / vein smooth muscle contraction / regulation of fever generation / sympathetic neuron axon guidance / response to prostaglandin F / glomerular endothelium development / positive regulation of sarcomere organization / noradrenergic neuron differentiation / semaphorin-plexin signaling pathway involved in axon guidance / histamine secretion / positive regulation of renal sodium excretion / leukocyte activation / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / positive regulation of penile erection / neuroblast migration / heparin metabolic process / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / posterior midgut development / regulation of D-glucose transmembrane transport / positive regulation of odontogenesis / epithelial fluid transport / response to leptin / 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 / endothelin receptor signaling pathway / response to ozone / developmental pigmentation / podocyte differentiation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / artery smooth muscle contraction / response to sodium phosphate / glomerular filtration / melanocyte differentiation / protein transmembrane transport / renal sodium excretion / enteric nervous system development / axonogenesis involved in innervation / positive regulation of cation channel activity / renin secretion into blood stream / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / renal albumin absorption / basal part of cell / positive regulation of smooth muscle contraction / respiratory gaseous exchange by respiratory system / peripheral nervous system development / regulation of pH / response to salt / positive regulation of urine volume / positive regulation of hormone secretion / negative regulation of adenylate cyclase activity / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / : / regulation of epithelial cell proliferation / negative regulation of blood coagulation / type 1 angiotensin receptor binding / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / superoxide anion generation / establishment of endothelial barrier / positive regulation of neutrophil chemotaxis / positive regulation of signaling receptor activity / cartilage development / middle ear morphogenesis / : / neural crest cell migration / 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
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 / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G protein alpha subunit / G-protein alpha subunit / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / 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. / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsTani, K. / Maki-Yonekura, S. / Kanno, R. / Negami, T. / Hamaguchi, T. / Hall, M. / Mizoguchi, A. / Humbel, B.M. / Terada, T. / Yonekura, K. / Doi, T.
Funding support Japan, 3items
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 ETB receptor-Gi complex in a conformation stabilized by the unique NPxxL motif
Authors: Tani, K. / Maki-Yonekura, S. / Kanno, R. / Negami, T. / Hamaguchi, T. / Hall, M. / Mizoguchi, A. / Humbel, B.M. / Terada, T. / Yonekura, K. / Doi, T.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Endothelin receptor type B
L: Endothelin-1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: SCFV16


Theoretical massNumber of molelcules
Total (without water)156,6516
Polymers156,6516
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC

#3: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40414.047 Da / Num. of mol.: 1 / Mutation: S47N, G203A, E245A, A326S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37671.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Protein / Protein/peptide / Antibody , 3 types, 3 molecules RLD

#1: Protein Endothelin receptor type B / ET-B / ET-BR / Endothelin receptor non-selective type


Mass: 38808.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDNRB, ETRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24530
#2: Protein/peptide Endothelin-1 / Preproendothelin-1 / PPET1


Mass: 2497.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05305
#6: Antibody SCFV16


Mass: 29398.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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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: ET-1 BOUND ETBR-GI COMPLEX / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 3.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1038215 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029266
ELECTRON MICROSCOPYf_angle_d0.45712555
ELECTRON MICROSCOPYf_dihedral_angle_d12.2843317
ELECTRON MICROSCOPYf_chiral_restr0.0381433
ELECTRON MICROSCOPYf_plane_restr0.0031579

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