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Yorodumi- PDB-3sph: Inward rectifier potassium channel Kir2.2 I223L mutant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sph | ||||||
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Title | Inward rectifier potassium channel Kir2.2 I223L mutant in complex with PIP2 | ||||||
Components | Inward-rectifier K+ channel Kir2.2 | ||||||
Keywords | METAL TRANSPORT / PIP / membrane protein / lipid / receptor | ||||||
Function / homology | Function and homology information Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å | ||||||
Authors | Hansen, S.B. / Tao, X. / MacKinnon, R. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structural basis of PIP(2) activation of the classical inward rectifier K(+) channel Kir2.2. Authors: Hansen, S.B. / Tao, X. / Mackinnon, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sph.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sph.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 3sph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sph_validation.pdf.gz | 722.2 KB | Display | wwPDB validaton report |
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Full document | 3sph_full_validation.pdf.gz | 726.4 KB | Display | |
Data in XML | 3sph_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3sph_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/3sph ftp://data.pdbj.org/pub/pdb/validation_reports/sp/3sph | HTTPS FTP |
-Related structure data
Related structure data | 3spcC 3spgSC 3spiC 3spjC 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: 39361.723 Da / Num. of mol.: 1 / Mutation: I223L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: Kir2.2 / Production host: Pichia pastoris (fungus) / References: UniProt: D2YW45, UniProt: F1NHE9*PLUS | ||
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#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PIO / [( | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.1% PEG400, 0.5 M potassium chloride, 0.05 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2010 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 12263 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SPG Resolution: 3.003→36.303 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 29.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.781 Å2 / ksol: 0.258 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.003→36.303 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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