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Yorodumi- PDB-6igk: Crystal Structure of human ETB receptor in complex with Endothelin-3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6igk | ||||||
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Title | Crystal Structure of human ETB receptor in complex with Endothelin-3 | ||||||
Components |
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Keywords | SIGNALING PROTEIN/PROTEIN BINDING / alpha helical / SIGNALING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information : / enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / chordate pharynx development / endothelin B receptor binding / peptide hormone secretion ...: / enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / chordate pharynx development / endothelin B receptor binding / peptide hormone secretion / vein smooth muscle contraction / regulation of fever generation / intracellular magnesium ion homeostasis / heparin metabolic process / positive regulation of penile erection / neuroblast migration / regulation of developmental pigmentation / posterior midgut development / epithelial fluid transport / podocyte differentiation / protein transmembrane transport / endothelin receptor signaling pathway / developmental pigmentation / renal sodium ion absorption / response to sodium phosphate / enteric nervous system development / renal sodium excretion / renin secretion into blood stream / multicellular organism development / renal albumin absorption / melanocyte differentiation / regulation of pH / positive regulation of potassium ion transmembrane transport / positive regulation of urine volume / positive regulation of leukocyte chemotaxis / negative regulation of adenylate cyclase activity / peripheral nervous system development / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / regulation of epithelial cell proliferation / type 1 angiotensin receptor binding / establishment of endothelial barrier / negative regulation of protein metabolic process / blood circulation / neural crest cell migration / response to pain / positive regulation of heart rate / macrophage chemotaxis / cGMP-mediated signaling / peptide hormone binding / regulation of vasoconstriction / canonical Wnt signaling pathway / viral release from host cell by cytolysis / regulation of heart rate / Peptide ligand-binding receptors / peptidoglycan catabolic process / neutrophil chemotaxis / positive regulation of mitotic nuclear division / calcium-mediated signaling / positive regulation of cell differentiation / calcium ion transmembrane transport / positive regulation of MAP kinase activity / intracellular calcium ion homeostasis / hormone activity / response to organic cyclic compound / neuron differentiation / vasodilation / cell wall macromolecule catabolic process / cell-cell signaling / lysozyme / lysozyme activity / gene expression / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / cellular response to lipopolysaccharide / host cell cytoplasm / cell surface receptor signaling pathway / defense response to bacterium / positive regulation of protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage RB59 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shihoya, W. / Izume, T. / Inoue, A. / Yamashita, K. / Kadji, F.M.N. / Hirata, K. / Aoki, J. / Nishizawa, T. / Nureki, O. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Crystal structures of human ETBreceptor provide mechanistic insight into receptor activation and partial activation. Authors: Shihoya, W. / Izume, T. / Inoue, A. / Yamashita, K. / Kadji, F.M.N. / Hirata, K. / Aoki, J. / Nishizawa, T. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6igk.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6igk.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 6igk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/6igk ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6igk | HTTPS FTP |
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-Related structure data
Related structure data | 6iglC 5glhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/611 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/611 |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 55956.727 Da / Num. of mol.: 1 Mutation: R124Y,D154A,K270A,C1052T,C1095A,S342A,I381A,C396A,C400A,C405A Source method: isolated from a genetically manipulated source Details: Chimera protein of Endothelin receptor type B inserted with Endolysin between residues 303 and 311. Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus) Gene: EDNRB, ETRB, e, RB59_126 / Plasmid: modified pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P24530, UniProt: A0A097J809, lysozyme | ||||
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#2: Protein/peptide | Mass: 2650.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14138 | ||||
#3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.91 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 500DME, Ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→49.599 Å / Num. obs: 46829 / % possible obs: 100 % / Redundancy: 204.625 % / Biso Wilson estimate: 35.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.858 / Rrim(I) all: 0.86 / Χ2: 1.401 / Net I/σ(I): 20.7 / Num. measured all: 9582405 / Scaling rejects: 4327 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GLH Resolution: 2→49.599 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.61 Å2 / Biso mean: 47.0245 Å2 / Biso min: 20.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→49.599 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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