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Yorodumi- PDB-4ovn: Voltage-gated Sodium Channel 1.5 (Nav1.5) C-terminal domain in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ovn | ||||||
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Title | Voltage-gated Sodium Channel 1.5 (Nav1.5) C-terminal domain in complex with Calmodulin poised for activation | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / SCN5A / Voltage Gated Sodium Channel / Calmodulin | ||||||
Function / homology | Function and homology information voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / regulation of ventricular cardiac muscle cell membrane depolarization ...voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / regulation of ventricular cardiac muscle cell membrane depolarization / cardiac ventricle development / membrane depolarization during atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / regulation of sodium ion transmembrane transport / brainstem development / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during AV node cell action potential / membrane depolarization during bundle of His cell action potential / positive regulation of action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / telencephalon development / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / : / establishment of protein localization to mitochondrial membrane / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / type 3 metabotropic glutamate receptor binding / membrane depolarization during action potential / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / CaM pathway / Interaction between L1 and Ankyrins / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / voltage-gated sodium channel activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ankyrin binding / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / sodium ion transport / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / fibroblast growth factor binding / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / membrane depolarization / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / intercalated disc / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / lateral plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / sodium ion transmembrane transport / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Gabelli, S.B. / Bianchet, M.A. / Boto, A. / Jakoncic, J. / Tomaselli, G.F. / Amzel, L.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2014 Title: Regulation of the NaV1.5 cytoplasmic domain by calmodulin. Authors: Gabelli, S.B. / Boto, A. / Kuhns, V.H. / Bianchet, M.A. / Farinelli, F. / Aripirala, S. / Yoder, J. / Jakoncic, J. / Tomaselli, G.F. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ovn.cif.gz | 838.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ovn.ent.gz | 720.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ovn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ovn_validation.pdf.gz | 541 KB | Display | wwPDB validaton report |
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Full document | 4ovn_full_validation.pdf.gz | 581.6 KB | Display | |
Data in XML | 4ovn_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 4ovn_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/4ovn ftp://data.pdbj.org/pub/pdb/validation_reports/ov/4ovn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 2 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 17321.496 Da / Num. of mol.: 5 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 Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS #2: Protein | Mass: 18642.982 Da / Num. of mol.: 5 / Fragment: C-terminal Domain (UNP residue 1773-1929) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN5A / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14524 |
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-Non-polymers , 4 types, 87 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.07 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 4K, 0.2 M MgSO4 and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.798→28.9 Å / Num. obs: 48516 / % possible obs: 90.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 77.01 Å2 / Rmerge(I) obs: 0.116 / Χ2: 78.182 / Net I/av σ(I): 32.384 / Net I/σ(I): 11.5 / Num. measured all: 311500 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.745 / Num. unique all: 2626 / Χ2: 0.089 / Rejects: 0 / % possible all: 58.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→28.7 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.42 Å2 / Biso mean: 93.06 Å2 / Biso min: 29.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→28.7 Å
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LS refinement shell | Resolution: 2.8→2.83 Å / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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