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- PDB-8zrt: Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-... -

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Basic information

Entry
Database: PDB / ID: 8zrt
TitleCryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex
Components
  • Endothelin receptor type B
  • Endothelin-1
KeywordsMEMBRANE PROTEIN / ENDOTHELIN / RECEPTOR / Gi / COMPLEX
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 / rhythmic excitation / neuroblast migration / negative regulation of phospholipase C/protein kinase C signal transduction / endothelin receptor activity / peptide hormone secretion ...enteric smooth muscle cell differentiation / response to endothelin / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / rhythmic excitation / neuroblast migration / negative regulation of phospholipase C/protein kinase C signal transduction / 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 / neural crest cell fate commitment / regulation of fever generation / vein smooth muscle contraction / response to prostaglandin F / glomerular endothelium development / sympathetic neuron axon guidance / noradrenergic neuron differentiation / histamine secretion / positive regulation of penile erection / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / leukocyte activation / rough endoplasmic reticulum lumen / posterior midgut development / phospholipase D-activating G protein-coupled receptor signaling pathway / body fluid secretion / positive regulation of sarcomere organization / regulation of D-glucose transmembrane transport / pharyngeal arch artery morphogenesis / endothelin receptor signaling pathway involved in heart process / positive regulation of odontogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / epithelial fluid transport / positive regulation of cation channel activity / heparin proteoglycan metabolic process / Weibel-Palade body / podocyte differentiation / response to ozone / endothelin receptor signaling pathway / renal sodium excretion / developmental pigmentation / positive regulation of cell growth involved in cardiac muscle cell development / response to leptin / response to sodium phosphate / axonogenesis involved in innervation / glomerular filtration / renin secretion into blood stream / cellular response to follicle-stimulating hormone stimulus / renal sodium ion absorption / renal albumin absorption / artery smooth muscle contraction / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / protein transmembrane transport / positive regulation of prostaglandin biosynthetic process / cellular response to mineralocorticoid stimulus / regulation of pH / melanocyte differentiation / positive regulation of smooth muscle contraction / respiratory gaseous exchange by respiratory system / positive regulation of renal sodium excretion / vasoconstriction / enteric nervous system development / basal part of cell / peripheral nervous system development / response to salt / type 1 angiotensin receptor binding / negative regulation of adenylate cyclase activity / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / regulation of epithelial cell proliferation / signal transduction involved in regulation of gene expression / dorsal/ventral pattern formation / embryonic heart tube development / axon extension / cellular response to toxic substance / cellular response to fatty acid / cartilage development / : / establishment of endothelial barrier / positive regulation of neutrophil chemotaxis / negative regulation of protein metabolic process / superoxide anion generation / cellular response to glucocorticoid stimulus / nitric oxide transport / neural crest cell migration / positive regulation of urine volume / response to pain / branching involved in blood vessel morphogenesis / response to dexamethasone / middle ear morphogenesis / response to testosterone / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx ...Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Endothelin-1 / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 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 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
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Endothelin receptor type B
L: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)41,3062
Polymers41,3062
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

#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
Has protein modificationY

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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 COMPLEX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401671 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032376
ELECTRON MICROSCOPYf_angle_d0.6793245
ELECTRON MICROSCOPYf_dihedral_angle_d4.07317
ELECTRON MICROSCOPYf_chiral_restr0.041402
ELECTRON MICROSCOPYf_plane_restr0.009388

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