+Open data
-Basic information
Entry | Database: PDB / ID: 5tzr | ||||||
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Title | GPR40 in complex with partial agonist MK-8666 | ||||||
Components | Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1 | ||||||
Keywords | FATTY ACID BINDING PROTEIN/HYDROLASE / FFAR1 / partial agonist / 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 / glucose homeostasis / lysozyme / 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 / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Lu, J. / Byrne, N. / Patel, S. / Sharma, S. / Soisson, S.M. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40. Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / ...Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / Hermes, J.D. / Ho, T. / Howard, A.D. / Josien, H. / Kornienko, M. / Lumb, K.J. / Miller, M.W. / Patel, S.B. / Pio, B. / Plummer, C.W. / Sherborne, B.S. / Sheth, P. / Souza, S. / Tummala, S. / Vonrhein, C. / Webb, M. / Allen, S.J. / Johnston, J.M. / Weinglass, A.B. / Sharma, S. / Soisson, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tzr.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tzr.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/5tzr ftp://data.pdbj.org/pub/pdb/validation_reports/tz/5tzr | HTTPS FTP |
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-Related structure data
Related structure data | 5tzyC 4phuS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53102.188 Da / Num. of mol.: 1 Mutation: L42A, F88A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: FFAR1, GPR40 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: O14842, UniProt: P00720, lysozyme |
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-Non-polymers , 6 types, 75 molecules
#2: Chemical | ChemComp-NA / | ||||
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#3: Chemical | ChemComp-MK6 / ( | ||||
#4: Chemical | ChemComp-MLI / | ||||
#5: Chemical | ChemComp-OLC / ( #6: Chemical | #7: 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: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.7 Details: 25-28%PEG 400, 0.2M sodium malonate, 0.1M Tris pH7.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 30519 / Biso Wilson estimate: 42.33 Å2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.507 / CC1/2: 0.788 / % possible all: 48.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4phu Resolution: 2.2→28.17 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.173
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Displacement parameters | Biso mean: 54.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→28.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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