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Yorodumi- PDB-5iwt: Structure of Transient Receptor Potential (TRP) channel TRPV6 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iwt | |||||||||
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Title | Structure of Transient Receptor Potential (TRP) channel TRPV6 in the presence of gadolinium | |||||||||
Components | Transient receptor potential cation channel subfamily V member 6 | |||||||||
Keywords | TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion ...parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | |||||||||
Authors | Saotome, K. / Singh, A.K. / Yelshanskaya, M.V. / Sobolevsky, A.I. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2016 Title: Crystal structure of the epithelial calcium channel TRPV6. Authors: Saotome, K. / Singh, A.K. / Yelshanskaya, M.V. / Sobolevsky, A.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iwt.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwt.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwt ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwt | HTTPS FTP |
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-Related structure data
Related structure data | 5iwkC 5iwpC 5iwrC 2rfaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 77148.469 Da / Num. of mol.: 1 / Mutation: I102Y, L132N, M136Q, L535Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv6 / Production host: Homo sapiens (human) / References: UniProt: Q9R186 | ||
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#2: Chemical | #3: Chemical | ChemComp-DTB / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 20-24% PEG 350 MME, 50 mM NaCl, and 50 mM Tris-HCl pH 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7101 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7101 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 22443 / % possible obs: 99.5 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 3.8→3.936 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RFA Resolution: 3.8→49.556 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 35.98 / Stereochemistry target values: ML
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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: 3.8→49.556 Å
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Refine LS restraints |
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LS refinement shell |
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