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Yorodumi- PDB-2kug: Halothane binds to druggable sites in calcium-calmodulin: Solutio... -
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-Basic information
Entry | Database: PDB / ID: 2kug | ||||||
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Title | Halothane binds to druggable sites in calcium-calmodulin: Solution Structure of halothane-CaM N-terminal domain | ||||||
Components | Calmodulin | ||||||
Keywords | METAL BINDING PROTEIN / CALMODULIN / CALCIUM BINDING / VOLATILE ANESTHETIC / HALOTHANE / Cytoskeleton / Isopeptide bond / Methylation / Phosphoprotein | ||||||
Function / homology | Function and homology information : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / 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 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, CHARMm22 energy minimization | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Juranic, N. / Macura, S. / Simeonov, M.V. / Jones, K.A. / Penheiter, A.R. / Hock, T.J. / Streiff, J.H. | ||||||
Citation | Journal: J. Serb. Chem. Soc. / Year: 2013 Title: Halothane binds to druggable sites in the [Ca2+]4-calmodulin (CaM) complex, but does not inhibit [Ca2+]4-CaM activation of kinase. Authors: Juranic, N.O. / Jones, K.A. / Penheiter, A.R. / Hock, T.J. / Streiff, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kug.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kug.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 2kug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/2kug ftp://data.pdbj.org/pub/pdb/validation_reports/ku/2kug | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8454.353 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN EF-hands 1 and 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: P62158, UniProt: P0DP23*PLUS | ||
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#2: Chemical | #3: Chemical | ChemComp-HLT / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The mechanism(s) of volatile anesthetic effects are poorly understood. We examined whether VA binding to druggable sites in calmodulin would effect [Ca2+]4-CaM dependent activity of enzymes. ...Details: The mechanism(s) of volatile anesthetic effects are poorly understood. We examined whether VA binding to druggable sites in calmodulin would effect [Ca2+]4-CaM dependent activity of enzymes. We used high resolution NMR spectroscopy to determine the structure of the halothane [Ca2+]4-CaM complex, determining that the halothane molecules bind in the druggable sites. We used fluorescence assays to determine that VA mediate [Ca2+]4-CaM activation of smMLCK, but not the kd of [Ca2+]4-CaM binding to skMLCK. These results suggest that VA do not mediate [Ca2+]4-CaM dependent MLCK activity via direct interactions with druggable sites on [Ca2+]4-CaM. | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, CHARMm22 energy minimization / Software ordinal: 1 / Details: 100 step steepest descent - final refinement | ||||||||||||
NMR constraints | NOE constraints total: 735 / NOE intraresidue total count: 314 / NOE long range total count: 128 / NOE medium range total count: 131 / NOE sequential total count: 157 / Hydrogen bond constraints total count: 74 / Protein chi angle constraints total count: 60 / Protein other angle constraints total count: 74 / Protein phi angle constraints total count: 75 / Protein psi angle constraints total count: 74 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 5 |