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Yorodumi- PDB-6mc9: Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mc9 | ||||||
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Title | Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin | ||||||
Components |
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Keywords | PROTEIN BINDING / SCN4A / voltage gated sodium channel / calmodulin / calmodulin-binding protein | ||||||
Function / homology | Function and homology information regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / establishment of protein localization to membrane / voltage-gated sodium channel complex / presynaptic cytosol / Interaction between L1 and Ankyrins / regulation of synaptic vesicle endocytosis / voltage-gated sodium channel activity ...regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / establishment of protein localization to membrane / voltage-gated sodium channel complex / presynaptic cytosol / Interaction between L1 and Ankyrins / regulation of synaptic vesicle endocytosis / voltage-gated sodium channel activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / sodium ion transport / nitric-oxide synthase binding / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / sodium ion transmembrane transport / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / : / titin binding / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / transmembrane transporter binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Yoder, J.B. / Gabelli, S.B. / Amzel, L.M. | ||||||
Funding support | United States, 1items
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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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mc9.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mc9.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/6mc9 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/6mc9 | HTTPS FTP |
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-Related structure data
Related structure data | 6mbaC 3g43S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19211.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P35499 |
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#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: pET24 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0DP29 |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VDCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→40.829 Å / Num. obs: 5845 / % possible obs: 99.9 % / Redundancy: 24.829 % / Biso Wilson estimate: 128.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.121 / Χ2: 1.008 / Net I/σ(I): 18.11 / Num. measured all: 145128 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G43 Resolution: 3.3→40.829 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 34.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 275.41 Å2 / Biso mean: 145.5062 Å2 / Biso min: 73.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→40.829 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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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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