+Open data
-Basic information
Entry | Database: PDB / ID: 8xwq | ||||||||||||
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Title | Cryo-EM structure of ET-1 bound ETBR-DNGI complex | ||||||||||||
Components |
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Keywords | MEMBRANE 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 | ||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
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. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xwq.cif.gz | 219.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xwq.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 8xwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xwq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8xwq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8xwq_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 8xwq_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/8xwq ftp://data.pdbj.org/pub/pdb/validation_reports/xw/8xwq | HTTPS FTP |
-Related structure data
Related structure data | 38741MC 8xwpC 8zrtC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC
#3: Protein | Mass: 40415.031 Da / Num. of mol.: 1 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 |
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#4: Protein | 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 | 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 |
-Protein / Protein/peptide / Antibody , 3 types, 3 molecules RLD
#1: Protein | 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 |
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#2: Protein/peptide | 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 | 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) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ET-1 BOUND ETBR-GI COMPLEX / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278209 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
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