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Yorodumi- PDB-4jpz: Voltage-gated sodium channel 1.2 C-terminal domain in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 4jpz | ||||||
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Title | Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and Ca2+/calmodulin | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / EF hand and IQ motif / ion channel / membrane | ||||||
Function / homology | Function and homology information establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of collateral sprouting / positive regulation of voltage-gated sodium channel activity / branching morphogenesis of a nerve / inhibitory synapse assembly / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / : / paranode region of axon ...establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of collateral sprouting / positive regulation of voltage-gated sodium channel activity / branching morphogenesis of a nerve / inhibitory synapse assembly / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / : / paranode region of axon / voltage-gated sodium channel complex / establishment of protein localization to mitochondrial membrane / negative regulation of microtubule depolymerization / dentate gyrus development / type 3 metabotropic glutamate receptor binding / node of Ranvier / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / 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 / beta-tubulin binding / sodium ion transport / voltage-gated calcium channel complex / 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 / microtubule polymerization / Phase 0 - rapid depolarisation / cerebral cortex cell migration / protein phosphatase activator activity / RHO GTPases activate PAKs / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / neuronal action potential / 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 / sodium channel regulator activity / DARPP-32 events / detection of calcium ion / intercalated disc / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / lateral plasma membrane / 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 / T-tubule / calcium channel complex / activation of adenylate cyclase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.02 Å | ||||||
Authors | Wang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Structural analyses of Ca(2+)/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation. Authors: Wang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jpz.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jpz.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 4jpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jpz ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jpz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21609.592 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF13, FHF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92913 #2: Protein | Mass: 21036.049 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN2A, NAC2, SCN2A1, SCN2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99250 #3: Protein | Mass: 16852.545 Da / Num. of mol.: 2 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 #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Sequence details | THE RESIDUES RRRP AT POSITIONS 59-62 ARE ISOFORM 2 NATURAL VARIANTS, UNP CODE Q92913-2 | |
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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: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 7.5 Details: 14% pEG3350, 300 mM sodium acetate,50 mM Tris pH 7.5, and 2 mM CaCl2, EVAPORATION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å | |||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012 | |||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.02→50 Å / Num. all: 53782 / Num. obs: 53782 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.02→48.23 Å / SU ML: 0.44 / σ(F): 1.4 / Phase error: 28.43 / 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: 3.02→48.23 Å
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Refine LS restraints |
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LS refinement shell |
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