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Yorodumi- PDB-8zrt: Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8zrt | ||||||||||||
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Title | Cryo-EM structure focused on the receptor of the 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) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 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 | 8zrt.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zrt.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 8zrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zrt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8zrt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8zrt_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 8zrt_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/8zrt ftp://data.pdbj.org/pub/pdb/validation_reports/zr/8zrt | HTTPS FTP |
-Related structure data
Related structure data | 60404MC 8xwpC 8xwqC 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
#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 |
-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 COMPLEX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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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.: 4 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
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 3.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401671 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
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