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Yorodumi- PDB-4yb9: Crystal structure of the Bovine Fructose transporter GLUT5 in an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yb9 | |||||||||
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Title | Crystal structure of the Bovine Fructose transporter GLUT5 in an open inward-facing conformation | |||||||||
Components | Solute carrier family 2, facilitated glucose transporter member 5 | |||||||||
Keywords | TRANSPORT PROTEIN / GLUT5 Transporter / Fructose / Bovine MFS / Open Inward-facing conformation | |||||||||
Function / homology | Function and homology information regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / cellular response to fructose stimulus / response to fructose / plasma membrane => GO:0005886 / sarcolemma / apical plasma membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Verdon, G. / Kang, H.J. / Iwata, S. / Drew, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2015 Title: Structure and mechanism of the mammalian fructose transporter GLUT5. Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. ...Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. / Kusano-Arai, O. / Iwanari, H. / Murata, T. / Kobayashi, T. / Hamakubo, T. / Kasahara, M. / Iwata, S. / Drew, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yb9.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yb9.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 4yb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4yb9 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4yb9 | HTTPS FTP |
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-Related 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: 52946.023 Da / Num. of mol.: 1 / Mutation: N51A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: SLC2A5, GLUT5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P58353 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.51 Å3/Da / Density % sol: 77.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: PEG 300, Hepes, Lithium Sulfate, Sodium Chloride, HEGA-10 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→33.317 Å / Num. obs: 13346 / % possible obs: 66.99 % / Redundancy: 10.2 % / Rsym value: 0.101 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rat GLUT5 crystal structure Resolution: 3.2→33.317 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.04 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→33.317 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.9302 Å / Origin y: -11.3213 Å / Origin z: -36.1469 Å
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Refinement TLS group | Selection details: all |