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Yorodumi- PDB-5ywy: Crystal structure of the human prostaglandin E receptor EP4 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ywy | |||||||||
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Title | Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and ONO-AE3-208 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN-IMMUNE SYSTEM / G-protein coupled receptor / lipid mediator / functional antibody / SIGNALING PROTEIN-IMMUNE SYSTEM complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of eosinophil extravasation / prostaglandin E receptor activity / Prostanoid ligand receptors / negative regulation of integrin activation / response to nematode / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / regulation of ossification / response to mechanical stimulus ...negative regulation of eosinophil extravasation / prostaglandin E receptor activity / Prostanoid ligand receptors / negative regulation of integrin activation / response to nematode / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / regulation of ossification / response to mechanical stimulus / JNK cascade / ERK1 and ERK2 cascade / bone development / positive regulation of cytokine production / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of inflammatory response / cellular response to prostaglandin E stimulus / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / response to lipopolysaccharide / inflammatory response / immune response / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Iwata, S. / Kobayashi, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2019 Title: Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface. Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / ...Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / Hotta, Y. / Asada, H. / Nakane, T. / Shiimura, Y. / Nakagita, T. / Tsuge, K. / Yoshida, S. / Kuribara, T. / Hosoya, T. / Sugimoto, Y. / Nomura, N. / Sato, M. / Hirokawa, T. / Kinoshita, M. / Murata, T. / Takayama, K. / Yamamoto, M. / Narumiya, S. / Iwata, S. / Kobayashi, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ywy.cif.gz | 297.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywy.ent.gz | 248.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ywy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ywy_validation.pdf.gz | 738.6 KB | Display | wwPDB validaton report |
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Full document | 5ywy_full_validation.pdf.gz | 747.8 KB | Display | |
Data in XML | 5ywy_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 5ywy_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywy ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywy | HTTPS FTP |
-Related structure data
Related structure data | 5yfiC 5yhlC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.1173791 / Data set type: diffraction image data / Details: Raw data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37063.547 Da / Num. of mol.: 1 Mutation: N7Q, A62L, G106R, N177Q, 218-259 deletion,N7Q, A62L, G106R, N177Q, 218-259 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGER4, PTGER2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35408 |
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#2: Antibody | Mass: 27574.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others) |
#3: Antibody | Mass: 26614.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others) |
#4: Chemical | ChemComp-7UR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.34 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 24-31% PEG 300, 150 mM potassium sulfate, 100 mM MES pH 5.5-6.5, 1% 1,2,3-heptantoriol PH range: 5.5-6.5 |
-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: RAYONIX MX225-HS / Detector: CCD / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 26463 / % possible obs: 99.9 % / Redundancy: 52 % / CC1/2: 0.997 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.2→3.33 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.879 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 253.38 Å2 / Biso mean: 82.0147 Å2 / Biso min: 14.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→48.879 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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