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Yorodumi- PDB-6iiv: Crystal structure of the human thromboxane A2 receptor bound to d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iiv | ||||||
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Title | Crystal structure of the human thromboxane A2 receptor bound to daltroban | ||||||
Components | Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor | ||||||
Keywords | SIGNALING PROTEIN / GPCR / Complex / Antagonist | ||||||
Function / homology | Function and homology information thromboxane A2 receptor activity / Prostanoid ligand receptors / : / positive regulation of smooth muscle contraction / positive regulation of blood pressure / negative regulation of cell migration involved in sprouting angiogenesis / response to testosterone / smooth muscle contraction / positive regulation of blood coagulation / positive regulation of vasoconstriction ...thromboxane A2 receptor activity / Prostanoid ligand receptors / : / positive regulation of smooth muscle contraction / positive regulation of blood pressure / negative regulation of cell migration involved in sprouting angiogenesis / response to testosterone / smooth muscle contraction / positive regulation of blood coagulation / positive regulation of vasoconstriction / response to nutrient / guanyl-nucleotide exchange factor activity / acrosomal vesicle / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of angiogenesis / G alpha (12/13) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / response to ethanol / cellular response to lipopolysaccharide / electron transfer activity / periplasmic space / nuclear speck / response to xenobiotic stimulus / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Fan, H. / Zhao, Q. / Wu, B. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat. Chem. Biol. / Year: 2019 Title: Structural basis for ligand recognition of the human thromboxane A2receptor. Authors: Fan, H. / Chen, S. / Yuan, X. / Han, S. / Zhang, H. / Xia, W. / Xu, Y. / Zhao, Q. / Wu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iiv.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iiv.ent.gz | 155.4 KB | Display | PDB format |
PDBx/mmJSON format | 6iiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iiv ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iiv | HTTPS FTP |
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-Related structure data
Related structure data | 6iiuC 1iroS 1m6tS 4pxzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53242.238 Da / Num. of mol.: 1 / Mutation: M1007W/H1102I/R1106L/L247A Source method: isolated from a genetically manipulated source Details: GPCR protein followed a traditional fusion strategy by introducing a bRIL fusion protein at the N terminus of the receptor and a rubredoxin fusion protein in the third intracellular loop of ...Details: GPCR protein followed a traditional fusion strategy by introducing a bRIL fusion protein at the N terminus of the receptor and a rubredoxin fusion protein in the third intracellular loop of the receptor. The residues from bRIL were numbered with 1001-1106 and the residues from rubredoxin were numbered with 2001 to 2054, with 2001 and 2054 covalently linked to residues 228 and 237 of the receptor, respectively. Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria) Gene: cybC, TBXA2R / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0ABE7, UniProt: P21731, UniProt: P00268 |
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#2: Chemical | ChemComp-A90 / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CLR / |
#5: Chemical | ChemComp-GOL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.94 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: Magnesium acetate, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 15664 / % possible obs: 97.2 % / Redundancy: 9.6 % / Biso Wilson estimate: 114.73 Å2 / Rmerge(I) obs: 0.242 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3→3.16 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PXZ, 1M6T, 1IRO Resolution: 3→48.35 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.891 / SU Rfree Blow DPI: 0.331 / SU Rfree Cruickshank DPI: 0.339
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Displacement parameters | Biso mean: 109.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→48.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 20.5457 Å / Origin y: 158.003 Å / Origin z: 139.023 Å
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Refinement TLS group | Selection details: { A|* } |