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Yorodumi- PDB-3sya: Crystal structure of the G protein-gated inward rectifier K+ chan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sya | ||||||
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Title | Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with sodium and PIP2 | ||||||
Components | G protein-activated inward rectifier potassium channel 2 | ||||||
Keywords | METAL TRANSPORT / ion channel / potassium channel / inward rectification / sodium binding / PIP2 binding / G protein binding | ||||||
Function / homology | Function and homology information G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma membrane ...G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma membrane / potassium channel activity / G-protein alpha-subunit binding / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / axon / dendrite / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Whorton, M.R. / MacKinnon, R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: Crystal Structure of the Mammalian GIRK2 K(+) Channel and Gating Regulation by G Proteins, PIP(2), and Sodium. Authors: Whorton, M.R. / Mackinnon, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sya.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sya.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 3sya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sya_validation.pdf.gz | 738.5 KB | Display | wwPDB validaton report |
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Full document | 3sya_full_validation.pdf.gz | 742.5 KB | Display | |
Data in XML | 3sya_validation.xml.gz | 14 KB | Display | |
Data in CIF | 3sya_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/3sya ftp://data.pdbj.org/pub/pdb/validation_reports/sy/3sya | HTTPS FTP |
-Related structure data
Related structure data | 3sycC 3syoC 3sypC 3syqC 2e4fS 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: 39061.957 Da / Num. of mol.: 1 / Fragment: UNP residues 52-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Girk2, Kcnj6, Kcnj7, W / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P48542 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-PIO / [( | ||
#4: Chemical | ChemComp-K / Sequence details | UNP P48542 S260T, I313M, AND M344L ARE NATURAL VARIANTS. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM sodium citrate, pH 6.0, 1 M sodium chloride, 20% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.975→41.727 Å / Num. obs: 13919 / % possible obs: 97.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.108 / Χ2: 1.217 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E4F Resolution: 2.98→41.727 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 33.296 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.724 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 289.75 Å2 / Biso mean: 100.8285 Å2 / Biso min: 42.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→41.727 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.975→3.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.12 Å / Origin y: -31.959 Å / Origin z: -37.842 Å
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