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Yorodumi- PDB-1u4f: Crystal Structure of Cytoplasmic Domains of IRK1 (Kir2.1) channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u4f | ||||||
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Title | Crystal Structure of Cytoplasmic Domains of IRK1 (Kir2.1) channel | ||||||
Components | Inward rectifier potassium channel 2 | ||||||
Keywords | ALLERGEN / cytoplasmic domain / Kir2.1 / IRK1 / inwardly rectifying K channel / rectification | ||||||
Function / homology | Function and homology information Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / cardiac muscle cell action potential / magnesium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / regulation of membrane repolarization ...Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / cardiac muscle cell action potential / magnesium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / regulation of membrane repolarization / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle cell contraction / relaxation of cardiac muscle / regulation of monoatomic ion transmembrane transport / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / intercalated disc / voltage-gated potassium channel complex / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transport / cellular response to mechanical stimulus / postsynaptic membrane / protein homotetramerization / dendritic spine / neuronal cell body / glutamatergic synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Pegan, S. / Arrabit, C. / Zhou, W. / Kwiatkowski, W. / Slesinger, P.A. / Choe, S. | ||||||
Citation | Journal: Nat Neurosci / Year: 2005 Title: Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. Authors: Scott Pegan / Christine Arrabit / Wei Zhou / Witek Kwiatkowski / Anthony Collins / Paul A Slesinger / Senyon Choe / Abstract: N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. ...N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. Two new crystal structures of the cytoplasmic domains of Kir2.1 (Kir2.1(L)) and the G protein-sensitive Kir3.1 (Kir3.1(S)) channels in the absence of PIP(2) show the cytoplasmic ion-permeation pathways occluded by four cytoplasmic loops that form a girdle around the central pore (G-loop). Significant flexibility of the pore-facing G-loop of Kir2.1(L) and Kir3.1(S) suggests a possible role as a diffusion barrier between cytoplasmic and transmembrane pores. Consistent with this, mutations of the G-loop disrupted gating or inward rectification. Structural comparison shows a di-aspartate cluster on the distal end of the cytoplasmic pore of Kir2.1(L) that is important for modulating inward rectification. Taken together, these results suggest the cytoplasmic domains of Kir channels undergo structural changes to modulate gating and inward rectification. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u4f.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u4f.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 1u4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u4f_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 1u4f_full_validation.pdf.gz | 479.4 KB | Display | |
Data in XML | 1u4f_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 1u4f_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u4f ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u4f | HTTPS FTP |
-Related structure data
Related structure data | 1u4eSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30840.580 Da / Num. of mol.: 4 / Fragment: Cytoplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj2, IRK1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35561 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: isopropanol, Tris-HCl, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2003 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. all: 42745 / Num. obs: 37871 / % possible obs: 88 % / Redundancy: 3.31 % / Rsym value: 0.054 / Net I/σ(I): 18.47 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U4E Resolution: 2.41→38.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.41→38.44 Å
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Refine LS restraints |
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