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- PDB-2kav: Solution structure of the human Voltage-gated Sodium Channel, bra... -

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Basic information

Entry
Database: PDB / ID: 2kav
TitleSolution structure of the human Voltage-gated Sodium Channel, brain isoform (Nav1.2)
ComponentsSodium channel protein type 2 subunit alpha
KeywordsTRANSPORT PROTEIN REGULATOR / Voltage-gated Sodium Channel / Alternative splicing / Disease mutation / Epilepsy / Glycoprotein / Ion transport / Ionic channel / Membrane / Polymorphism / Sodium / Sodium channel / Sodium transport / Transmembrane / Transport / Ubl conjugation / Voltage-gated channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / paranode region of axon / voltage-gated sodium channel complex / dentate gyrus development / node of Ranvier / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport ...intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / paranode region of axon / voltage-gated sodium channel complex / dentate gyrus development / node of Ranvier / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport / voltage-gated calcium channel complex / Phase 0 - rapid depolarisation / calcium ion import across plasma membrane / neuronal action potential / intercalated disc / T-tubule / myelination / determination of adult lifespan / Sensory perception of sweet, bitter, and umami (glutamate) taste / memory / presynaptic membrane / nervous system development / cellular response to hypoxia / neuron apoptotic process / calmodulin binding / axon / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / 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 / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site ...Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / 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 / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 / Ion transport domain / Ion transport protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sodium channel protein type 2 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiloushev, V.Z. / Levine, J.A. / Arbing, M.A. / Hunt, J.F. / Pitt, G.S. / Palmer, A.G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Solution structure of the NaV1.2 C-terminal EF-hand domain.
Authors: Miloushev, V.Z. / Levine, J.A. / Arbing, M.A. / Hunt, J.F. / Pitt, G.S. / Palmer, A.G.
History
DepositionNov 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium channel protein type 2 subunit alpha


Theoretical massNumber of molelcules
Total (without water)14,5911
Polymers14,5911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sodium channel protein type 2 subunit alpha / / Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2 / ...Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2 / Sodium channel protein / brain II subunit alpha / HBSC II


Mass: 14591.391 Da / Num. of mol.: 1 / Fragment: C-terminal EF-Hand Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: NAC2, SCN2A, SCN2A1, SCN2A2 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99250

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the human Voltage-gated Sodium Channel, brain isoform (Nav1.2)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11122D 1H-13C HSQC
11233D HCACO
11332D IPAP HSQC
11433D quant HNCO
11533D CCa HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-10% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 15 mg pF1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein[U-99% 13C; U-99% 15N]1
100 mMglycine[D5-98%]1
20 mMTRIS[D11-98 %]1
0.1 mMEDTA[D16-98%]1
10 %D2O[U-99% 2H]1
1 mMDTT[D10-98%]1
0.02 %NaN31
0.5 mMprotein[U-10% 13C; U-99% 15N]2
100 mMglycine[D5-98%]2
20 mMTRIS[D11-98 %]2
0.1 mMEDTA[D16-98%]2
10 %D2O[U-99% 2H]2
1 mMDTT[D10-98%]2
0.02 %NaN32
0.5 mMprotein[U-99% 13C; U-99% 15N]3
100 mMglycine[D5-98%]3
20 mMTRIS[D11-98 %]3
0.1 mMEDTA[D16-98%]3
10 %D2O[U-99% 2H]3
1 mMDTT[D10-98%]3
0.02 %NaN33
15 mg/mLpF1 phage3
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 290.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
ARIA2.2Linge, O'Donoghue and Nilgesinitial structure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readinitial structure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: XPLOR-NIH (2.18) Internal Variables Module, refine.py script (CDS 2005/05/10)
NMR constraintsNOE constraints total: 1772 / NOE intraresidue total count: 699 / NOE long range total count: 310 / NOE medium range total count: 321 / NOE sequential total count: 442 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.071 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0.25 Å / Maximum torsion angle constraint violation: 6.99 ° / Maximum upper distance constraint violation: 0.42 Å
Torsion angle constraint violation method: ensemble average of rmsd
NMR ensemble rmsDistance rms dev: 0.021 Å / Distance rms dev error: 0.021 Å

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