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- PDB-5jr0: Domain 4 Segment 6 of voltage-gated sodium channel Nav1.4 -

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Basic information

Entry
Database: PDB / ID: 5jr0
TitleDomain 4 Segment 6 of voltage-gated sodium channel Nav1.4
ComponentsSodium channel protein type 4 subunit alpha
KeywordsMETAL BINDING PROTEIN / transmembrane / alpha-helix / protein fragment
Function / homology
Function and homology information


regulation of skeletal muscle contraction by action potential / choline transport / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / sodium ion transport / neuronal action potential / monoatomic cation transport ...regulation of skeletal muscle contraction by action potential / choline transport / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / sodium ion transport / neuronal action potential / monoatomic cation transport / sodium ion transmembrane transport / potassium ion transport / axon / plasma membrane
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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 4 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsNiitsu, A. / Egawa, A. / Ikeda, K. / Tachibana, K. / Fujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: To Be Published
Title: Veratridine binding to a transmembrane segment of mammalian sodium channel Nav1.4 determined by solid-state NMR
Authors: Niitsu, A. / Egawa, A. / Ikeda, K. / Tachibana, K. / Fujiwara, T.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium channel protein type 4 subunit alpha


Theoretical massNumber of molelcules
Total (without water)4,0331
Polymers4,0331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide Sodium channel protein type 4 subunit alpha / / Mu-1 / SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV ...Mu-1 / SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.4


Mass: 4033.070 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1567-1594 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P15390

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic113C-13C dipolar-assisted rotational resonance
122anisotropic113C-13C dipolar-assisted rotational resonance
131anisotropic113C observation of 2H-selective 1H-depolarization

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
liposome116 % U-13C I23, L17, V20 peptide, 69 % d-54 DMPC, waterLabel1water
liposome216 % U-13C G, I, F, L, V, A peptide, 69 % d-54 DMPC, waterLabel2water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
16 %peptideU-13C I23, L17, V201
69 %DMPCd-541
16 %peptideU-13C G, I, F, L, V, A2
69 %DMPCd-542
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 7.4 Not defined / Pressure: 1 atm / Temperature: 213 K

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NMR measurement

NMR spectrometerType: Varian Infinity Plus 700 / Manufacturer: Varian / Model: Infinity Plus 700 / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CHARMMM. KARPLUS ET AL, HARVARD UNIVERSITYrefinement
FELIXstructure solution
DELTAstructure solution
SPARKYstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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