|Entry||Database: PDB / ID: 6mba|
|Title||Crystal Structure of Human Nav1.4 CTerminal Domain in Complex with apo Calmodulin|
|Keywords||CALMODULIN-BINDING PROTEIN / SCN4A / voltage gated sodium channel / calmodulin / MEMBRANE PROTEIN|
|Function / homology|
Function and homology information
regulation of skeletal muscle contraction by action potential / regulation of store-operated calcium channel activity / voltage-gated sodium channel complex / membrane depolarization during action potential / regulation of high voltage-gated calcium channel activity / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / neuronal action potential / establishment of protein localization to membrane ...regulation of skeletal muscle contraction by action potential / regulation of store-operated calcium channel activity / voltage-gated sodium channel complex / membrane depolarization during action potential / regulation of high voltage-gated calcium channel activity / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / neuronal action potential / establishment of protein localization to membrane / calcium channel regulator activity / voltage-gated ion channel activity / establishment of protein localization to mitochondrial membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Phase 0 - rapid depolarisation / N-terminal myristoylation domain binding / type 3 metabotropic glutamate receptor binding / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / sodium ion transmembrane transport / positive regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / positive regulation of cyclic-nucleotide phosphodiesterase activity / adenylate cyclase binding / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / calcium channel inhibitor activity / adenylate cyclase activator activity / regulation of ion transmembrane transport / positive regulation of phosphoprotein phosphatase activity / activation of adenylate cyclase activity / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of heart rate / titin binding / sarcomere / positive regulation of protein dephosphorylation / calcium channel complex / phosphatidylinositol 3-kinase binding / response to amphetamine / regulation of ryanodine-sensitive calcium-release channel activity / enzyme regulator activity / calcium-mediated signaling / regulation of cytokinesis / nitric-oxide synthase regulator activity / regulation of synaptic vesicle exocytosis / positive regulation of DNA binding / myelin sheath / muscle contraction / spindle microtubule / response to calcium ion / spindle pole / calcium-dependent protein binding / positive regulation of nitric-oxide synthase activity / growth cone / disordered domain specific binding / G2/M transition of mitotic cell cycle / transmembrane transporter binding / protein N-terminus binding / centrosome / neuron projection / axon / protein domain specific binding / calcium ion binding / protein kinase binding / integral component of plasma membrane / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Voltage gated sodium channel, alpha-4 subunit, mammalian / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / EF-hand domain pair ...Voltage gated sodium channel, alpha-4 subunit, mammalian / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / EF-hand domain pair / Ion transport protein / Ion transport domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain profile. / EF-hand calcium-binding domain. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
CARBONATE ION / Calmodulin-1 / Sodium channel protein type 4 subunit alpha
Similarity search - Component
|Biological species||Homo sapiens (human)|
Rattus norvegicus (Norway rat)
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å|
|Authors||Yoder, J. / Gabelli, S.B. / Amzel, L.M.|
|Funding support|| United States, 1items |
|Citation||Journal: Nat Commun / Year: 2019|
Title: Ca2+-dependent regulation of sodium channels NaV1.4 and NaV1.5 is controlled by the post-IQ motif.
Authors: Yoder, J.B. / Ben-Johny, M. / Farinelli, F. / Srinivasan, L. / Shoemaker, S.R. / Tomaselli, G.F. / Gabelli, S.B. / Amzel, L.M.
|Structure viewer||Molecule: |
Downloads & links
A: Sodium channel protein type 4 subunit alpha
|Components on special symmetry positions|
-Protein , 2 types, 2 molecules A
|#1: Protein|| |
Mass: 19607.188 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P35499
|#2: Protein|| |
Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI / Plasmid: pET-24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P0DP29
-Non-polymers , 5 types, 127 molecules
|#4: Chemical|| ChemComp-EDO / ||#5: Chemical|| ChemComp-CO3 / ||#6: Chemical|| ChemComp-TRS / ||#7: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 1.77 Å3/Da / Density % sol: 30.7 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl|
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.918 Å|
|Detector||Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2017|
|Radiation||Monochromator: VDCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.918 Å / Relative weight: 1|
|Reflection||Resolution: 1.799→44.875 Å / Num. obs: 42682 / % possible obs: 91.4 % / Redundancy: 1.605 % / Biso Wilson estimate: 39.247 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.084 / Χ2: 1.189 / Net I/σ(I): 6.57|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4OVN
Resolution: 1.799→44.875 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 25.23
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.799→44.875 Å|
|Refine LS restraints|
|LS refinement shell|
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
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