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Yorodumi- PDB-1g4y: 1.60 A CRYSTAL STRUCTURE OF THE GATING DOMAIN FROM SMALL CONDUCTA... -
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-Basic information
Entry | Database: PDB / ID: 1g4y | ||||||
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Title | 1.60 A CRYSTAL STRUCTURE OF THE GATING DOMAIN FROM SMALL CONDUCTANCE POTASSIUM CHANNEL COMPLEXED WITH CALCIUM-CALMODULIN | ||||||
Components |
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Keywords | SIGNALING PROTEIN / small-conductance calcium-activated potassium channel / calmodulin / calmodulin binding domain (CaMBD) / channel gating | ||||||
Function / homology | Function and homology information Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / positive regulation of potassium ion transport / inward rectifier potassium channel activity / type 3 metabotropic glutamate receptor binding / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / smooth endoplasmic reticulum / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / T-tubule / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / potassium ion transport / modulation of chemical synaptic transmission / spindle microtubule / sarcolemma / Z disc / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / postsynaptic membrane / vesicle / transmembrane transporter binding / protein autophosphorylation / dendritic spine / calmodulin binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / neuronal cell body / glutamatergic synapse / calcium ion binding / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Schumacher, M.A. / Rivard, A. / Bachinger, H.P. / Adelman, J.P. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin. Authors: Schumacher, M.A. / Rivard, A.F. / Bachinger, H.P. / Adelman, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g4y.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g4y.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1g4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g4y_validation.pdf.gz | 392 KB | Display | wwPDB validaton report |
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Full document | 1g4y_full_validation.pdf.gz | 397 KB | Display | |
Data in XML | 1g4y_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1g4y_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g4y ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g4y | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | the relevant dimer is generated by crystallographic symmetry. |
-Components
#1: Protein | Mass: 12105.248 Da / Num. of mol.: 1 / Fragment: CALMODULIN-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RAT / Plasmid: PET23B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604 | ||
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#2: Protein | Mass: 16721.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RAT / Plasmid: PET33B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: 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: 2.9 Å3/Da / Density % sol: 57.57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium sulphate, lithium sulphate, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2000 / Details: mirrors |
Radiation | Monochromator: double-crystal Si 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 115320 / Num. obs: 40694 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 5 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5200 / Rsym value: 28.9 / % possible all: 87.9 |
Reflection | *PLUS Num. measured all: 115320 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: room temp model Resolution: 1.6→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh and huber
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Displacement parameters | Biso mean: 4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 4 Å2 |