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Yorodumi- PDB-3spc: Inward rectifier potassium channel Kir2.2 in complex with dioctan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3spc | ||||||
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Title | Inward rectifier potassium channel Kir2.2 in complex with dioctanoylglycerol pyrophosphate (DGPP) | ||||||
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: 2.454 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 | 3spc.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3spc.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 3spc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3spc_validation.pdf.gz | 670.4 KB | Display | wwPDB validaton report |
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Full document | 3spc_full_validation.pdf.gz | 674.3 KB | Display | |
Data in XML | 3spc_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3spc_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/3spc ftp://data.pdbj.org/pub/pdb/validation_reports/sp/3spc | HTTPS FTP |
-Related structure data
Related structure data | 3spgC 3sphC 3spiC 3spjC 3jycS 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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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 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-P8P / ( | #4: 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: 4.17 Å3/Da / Density % sol: 70.52 % |
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Crystal grow | Method: hanging drop, vapor diffusion / pH: 7 Details: 6.2% PEG400, 0.5 M potassium chloride, 0.1 M HEPES, pH 7.0, HANGING DROP, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2011 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→16 Å / Num. obs: 23341 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rsym value: 0.146 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3JYC Resolution: 2.454→15.657 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 22.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.91 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.454→15.657 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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