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Yorodumi- PDB-1qx7: Crystal structure of apoCaM bound to the gating domain of small c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qx7 | ||||||
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Title | Crystal structure of apoCaM bound to the gating domain of small conductance Ca2+-activated potassium channel | ||||||
Components |
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Keywords | SIGNALING PROTEIN / apoCalmodulin / SK channel / small conductance Ca2+ activated K+ channel / CaMBD / gating domain / Ca2+-activated gating / functioanl bipartism | ||||||
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 / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of neuronal synaptic plasticity / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / alpha-actinin binding / protein phosphatase activator activity / smooth endoplasmic reticulum / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / T-tubule / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / sarcolemma / modulation of chemical synaptic transmission / potassium ion transport / Z disc / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / postsynaptic membrane / vesicle / transmembrane transporter binding / dendritic spine / protein autophosphorylation / 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 / molecular replacement combined with MAD / Resolution: 3.09 Å | ||||||
Authors | Schumacher, M.A. / Crum, M. / Miller, M.C. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex. Authors: Schumacher, M.A. / Crum, M. / Miller, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qx7.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qx7.ent.gz | 120.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/1qx7 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qx7 | HTTPS FTP |
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-Related structure data
Related structure data | 1qx5SC 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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2 |
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3 |
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4 |
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Unit cell |
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Details | the apoCaM/CaMBD complex is monomeric, also in the crystal are two domain swapped dimers of apoCaM which "anchor" the flexible apoCaM/CaMBD complex |
-Components
#1: Protein | Mass: 17143.406 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Gene: CALM1, CAM1, CALM, CAM, CALM2, CAM2, CAMB, CALM3, CAM3, CAMC Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS #2: Protein | | Mass: 10216.989 Da / Num. of mol.: 1 / Fragment: SK2 gating domain (residues 411-487) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: KCNN2 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604 |
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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: 1.84 Å3/Da / Density % sol: 33.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Citrate, NaCl, Hepes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.05 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→75.16 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.09→3.51 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement combined with MAD Starting model: 1QX5 Resolution: 3.09→75.16 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3330198.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 83.9875 Å2 / ksol: 0.365198 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.09→75.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.51 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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