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Yorodumi- PDB-5iwp: Structure of Transient Receptor Potential (TRP) channel TRPV6 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iwp | |||||||||
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Title | Structure of Transient Receptor Potential (TRP) channel TRPV6 in the presence of calcium | |||||||||
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 / response to calcium ion / calcium channel activity ...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 / response to calcium ion / calcium channel activity / 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: 3.65 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 | 5iwp.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwp.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iwp_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 5iwp_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 5iwp_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5iwp_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwp ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwp | HTTPS FTP |
-Related structure data
Related structure data | 5iwkC 5iwrC 5iwtC 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, 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 PH range: 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: 1.75 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.75 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→49.56 Å / Num. obs: 25439 / % possible obs: 99.9 % / Redundancy: 26.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.01 / Net I/σ(I): 25 |
Reflection shell | Resolution: 3.65→3.78 Å / Redundancy: 17.2 % / Rmerge(I) obs: 1.431 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RFA Resolution: 3.65→49.556 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.48 / 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: 3.65→49.556 Å
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Refine LS restraints |
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LS refinement shell |
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