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Yorodumi- PDB-5kw2: The extra-helical binding site of GPR40 and the structural basis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kw2 | ||||||
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Title | The extra-helical binding site of GPR40 and the structural basis for allosteric agonism and incretin stimulation | ||||||
Components | Free fatty acid receptor 1,Lysozyme,Free fatty acid receptor 1 | ||||||
Keywords | Fatty acid binding protein/Hydrolase / G-protein coupled receptor / free fatty acid receptor 1 / lipid-binding protein / Fatty acid binding protein-Hydrolase complex | ||||||
Function / homology | Function and homology information bioactive lipid receptor activity / Free fatty acid receptors / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / ion channel modulating, G protein-coupled receptor signaling pathway / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / response to fatty acid / positive regulation of calcium ion transport / insulin secretion / negative regulation of interleukin-1 beta production / ligand-gated ion channel signaling pathway ...bioactive lipid receptor activity / Free fatty acid receptors / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / ion channel modulating, G protein-coupled receptor signaling pathway / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / response to fatty acid / positive regulation of calcium ion transport / insulin secretion / negative regulation of interleukin-1 beta production / ligand-gated ion channel signaling pathway / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled receptor activity / positive regulation of insulin secretion / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / cell wall macromolecule catabolic process / lysozyme / glucose homeostasis / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / lipid binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Ho, J.D. / Chau, B. / Rodgers, L. / Lu, F. / Wilbur, K.L. / Otto, K.A. / Chen, Y. / Song, M. / Riley, J.P. / Yang, H.-C. ...Ho, J.D. / Chau, B. / Rodgers, L. / Lu, F. / Wilbur, K.L. / Otto, K.A. / Chen, Y. / Song, M. / Riley, J.P. / Yang, H.-C. / Reynolds, N.A. / Kahl, S.D. / Lewis, A.P. / Groshong, C. / Madsen, R.E. / Conners, K. / Linswala, J.P. / Gheyi, T. / Saflor, M.D. / Lee, M.R. / Benach, J. / Baker, K.A. / Montrose-Rafizadeh, C. / Genin, M.J. / Miller, A.R. / Hamdouchi, C. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for GPR40 allosteric agonism and incretin stimulation. Authors: Ho, J.D. / Chau, B. / Rodgers, L. / Lu, F. / Wilbur, K.L. / Otto, K.A. / Chen, Y. / Song, M. / Riley, J.P. / Yang, H.C. / Reynolds, N.A. / Kahl, S.D. / Lewis, A.P. / Groshong, C. / Madsen, R. ...Authors: Ho, J.D. / Chau, B. / Rodgers, L. / Lu, F. / Wilbur, K.L. / Otto, K.A. / Chen, Y. / Song, M. / Riley, J.P. / Yang, H.C. / Reynolds, N.A. / Kahl, S.D. / Lewis, A.P. / Groshong, C. / Madsen, R.E. / Conners, K. / Lineswala, J.P. / Gheyi, T. / Saflor, M.D. / Lee, M.R. / Benach, J. / Baker, K.A. / Montrose-Rafizadeh, C. / Genin, M.J. / Miller, A.R. / Hamdouchi, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kw2.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kw2.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kw2_validation.pdf.gz | 740 KB | Display | wwPDB validaton report |
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Full document | 5kw2_full_validation.pdf.gz | 742.3 KB | Display | |
Data in XML | 5kw2_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5kw2_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/5kw2 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kw2 | HTTPS FTP |
-Related structure data
Related structure data | 4phuS S: Starting model for refinement |
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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: 53102.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: FFAR1, GPR40, e, T4Tp126 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O14842, UniProt: D9IEF7, lysozyme |
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#2: Chemical | ChemComp-6XQ / ( |
#3: 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: 3.12 Å3/Da / Density % sol: 60.54 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase Details: 0.1 M Tris HCl, pH 8.5, 30% PEG 400, 0.2 M ammonium formate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 2, 2016 |
Radiation | Monochromator: Kohzu HLD-4 with diamond 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→19.81 Å / Num. obs: 16090 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rsym value: 0.13 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.76→2.91 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PHU Resolution: 2.76→19.81 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.455 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.658 / ESU R Free: 0.344
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.61 Å2 / Biso mean: 41.374 Å2 / Biso min: 13.68 Å2
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Refinement step | Cycle: final / Resolution: 2.76→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.764→2.834 Å / Total num. of bins used: 20
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