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Yorodumi- PDB-4qnh: Calcium-calmodulin (T79D) complexed with the calmodulin binding d... -
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-Basic information
Entry | Database: PDB / ID: 4qnh | ||||||
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Title | Calcium-calmodulin (T79D) complexed with the calmodulin binding domain from a small conductance potassium channel SK2-a | ||||||
Components |
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Keywords | ion transport/protein binding / ion channel / ion transport-protein binding complex | ||||||
Function / homology | Function and homology information Cam-PDE 1 activation / eNOS activation / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / RHO GTPases activate IQGAPs / Glycogen breakdown (glycogenolysis) / : / CaMK IV-mediated phosphorylation of CREB / Calcineurin activates NFAT / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...Cam-PDE 1 activation / eNOS activation / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / RHO GTPases activate IQGAPs / Glycogen breakdown (glycogenolysis) / : / CaMK IV-mediated phosphorylation of CREB / Calcineurin activates NFAT / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CLEC7A (Dectin-1) induces NFAT activation / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Activation of RAC1 downstream of NMDARs / Protein methylation / : / Stimuli-sensing channels / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calmodulin induced events / Ca2+ activated K+ channels / Smooth Muscle Contraction / FCERI mediated Ca+2 mobilization / small conductance calcium-activated potassium channel activity / Platelet degranulation / RAF activation / Synthesis of IP3 and IP4 in the cytosol / PKA activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / Phase 0 - rapid depolarisation / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / Inactivation, recovery and regulation of the phototransduction cascade / Extra-nuclear estrogen signaling / 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 / Activation of Ca-permeable Kainate Receptor / Ca2+ pathway / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / RAF/MAP kinase cascade / 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 / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Ion homeostasis / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / alpha-actinin binding / regulation of neuronal synaptic plasticity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / smooth endoplasmic reticulum / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / Unblocking of NMDA receptors, glutamate binding and activation / phosphatidylinositol 3-kinase binding / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / T-tubule / calcium channel complex / activation of adenylate cyclase activity / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / potassium ion transport / modulation of chemical synaptic transmission / sarcolemma / spindle pole Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Zhang, M. / Pascal, J.M. / Logothetis, D.E. / Zhang, J.F. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 Title: Selective phosphorylation modulates the PIP2 sensitivity of the CaM-SK channel complex. Authors: Zhang, M. / Meng, X.Y. / Cui, M. / Pascal, J.M. / Logothetis, D.E. / Zhang, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qnh.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qnh.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qnh_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 4qnh_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 4qnh_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4qnh_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/4qnh ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qnh | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12243.395 Da / Num. of mol.: 1 / Fragment: Calmodulin binding domain (UNP residues 396-487) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P70604 | ||
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#2: Protein | Mass: 16866.529 Da / Num. of mol.: 1 / Mutation: T79D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP31*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: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 5.6 Details: 1.5 M Li2SO4, 0.5 M (NH4)2SO4, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2013 |
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→26.65 Å / Num. all: 21057 / Num. obs: 21057 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 |
Reflection shell | Resolution: 2.02→2.07 Å / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→26.648 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→26.648 Å
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Refine LS restraints |
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LS refinement shell |
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