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Yorodumi- PDB-5tp6: Solution structure of the CaM34 with the iNOS CaM binding domain ... -
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-Basic information
Entry | Database: PDB / ID: 5tp6 | ||||||
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Title | Solution structure of the CaM34 with the iNOS CaM binding domain peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Calcium deficient / nitric oxide synthase | ||||||
Function / homology | Function and homology information positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine 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 / cortical cytoskeleton / superoxide metabolic process / 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 / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / peroxisomal matrix / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / regulation of insulin secretion / 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 / nitric-oxide synthase (NADPH) / 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 / nitric-oxide synthase 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 / nitric oxide mediated signal transduction / arginine catabolic process / 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 / negative regulation of blood pressure / nitric oxide biosynthetic process / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / response to hormone Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Piazza, M. / Dieckmann, T. / Guillemette, J.G. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structural Consequences of Calmodulin EF Hand Mutations. Authors: Piazza, M. / Taiakina, V. / Dieckmann, T. / Guillemette, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tp6.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5tp6.ent.gz | 1020.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tp6 ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tp6 | HTTPS FTP |
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-Related structure data
Related structure data | 5tp5C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16633.330 Da / Num. of mol.: 1 / Mutation: D93A, D129A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS |
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#2: Protein/peptide | Mass: 3402.371 Da / Num. of mol.: 1 / Fragment: residues 507-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOS2, NOS2A / Production host: Escherichia coli (E. coli) / References: UniProt: P35228, nitric-oxide synthase (NADPH) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1 mM [U-99% 13C; U-99% 15N] CaM34, 1 mM iNOS CaM binding domain peptide, 100 mM potassium chloride, 10 mM Calcium chloride, 0.2 mM sodium azide, 90% H2O/10% D2O Label: CaM34iNOS / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: conditions 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 20 |