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Yorodumi- PDB-5oeo: Solution structure of the complex of TRPV5(655-725) with a Calmod... -
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-Basic information
Entry | Database: PDB / ID: 5oeo | ||||||||||||||||||
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Title | Solution structure of the complex of TRPV5(655-725) with a Calmodulin E32Q/E68Q double mutant | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / TRPV5 / calcium channel / dynamics / calmodulin / regulation | ||||||||||||||||||
Function / homology | Function and homology information regulation of urine volume / TRP channels / 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 / Loss of phosphorylation of MECP2 at T308 ...regulation of urine volume / TRP channels / 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 / 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 / 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / 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 / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / 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 / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / Protein methylation / voltage-gated potassium channel complex / 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 / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / calcium ion transmembrane transport / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel activity / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium ion transport / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | SOLUTION NMR / simulated annealing / molecular dynamics | ||||||||||||||||||
Authors | Vuister, G.W. / Bokhovchuk, F.M. / Bate, N. / Kovalevskaya, N. / Goult, B.T. / Spronk, C.A.E.M. | ||||||||||||||||||
Funding support | United Kingdom, Netherlands, 5items
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Citation | Journal: Biochemistry / Year: 2018 Title: The Structural Basis of Calcium-Dependent Inactivation of the Transient Receptor Potential Vanilloid 5 Channel. Authors: Bokhovchuk, F.M. / Bate, N. / Kovalevskaya, N.V. / Goult, B.T. / Spronk, C.A.E.M. / Vuister, G.W. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oeo.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oeo.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5oeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oeo ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oeo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 16937.652 Da / Num. of mol.: 1 / Mutation: E32Q, E68Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DP23 |
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#2: Protein | Mass: 7722.194 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV5, ECAC1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NQA5 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 84 mM / Ionic strength err: 0.01 / Label: NMR Buffer / pH: 7.4 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 308 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 120 / Conformers submitted total number: 20 |