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- PDB-2kbi: Solution NMR structure of the C-terminal EF-hand domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2kbi
TitleSolution NMR structure of the C-terminal EF-hand domain of human cardiac sodium channel NaV1.5
ComponentsSodium channel protein type 5 subunit alpha
KeywordsMETAL BINDING PROTEIN / protein / EF-hand / sodium channel / Brugada syndrome / Cardiomyopathy / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Long QT syndrome / Membrane / Phosphoprotein / Polymorphism / Sodium / Sodium transport / Transmembrane / Transport / Ubl conjugation / Voltage-gated channel
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 / cardiac ventricle development / response to denervation involved in regulation of muscle adaptation ...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 / cardiac ventricle development / response to denervation involved in regulation of muscle adaptation / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of atrial cardiac muscle cell membrane repolarization / membrane depolarization during atrial cardiac muscle cell action potential / membrane depolarization during action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / membrane depolarization during AV node cell action potential / regulation of sodium ion transmembrane transport / membrane depolarization during bundle of His cell action potential / brainstem development / membrane depolarization during Purkinje myocyte cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / positive regulation of action potential / atrial cardiac muscle cell action potential / telencephalon development / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle cell action potential / high voltage-gated calcium channel activity / regulation of cardiac muscle cell contraction / voltage-gated sodium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / Interaction between L1 and Ankyrins / ankyrin binding / sodium ion transport / fibroblast growth factor binding / voltage-gated calcium channel complex / nitric-oxide synthase binding / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / odontogenesis of dentin-containing tooth / calcium ion import across plasma membrane / membrane depolarization / sodium ion transmembrane transport / intercalated disc / lateral plasma membrane / cardiac muscle contraction / T-tubule / cellular response to calcium ion / regulation of heart rate / cerebellum development / positive regulation of epithelial cell proliferation / caveola / sarcolemma / Z disc / scaffold protein binding / transmembrane transporter binding / calmodulin binding / protein domain specific binding / ubiquitin protein ligase binding / nucleolus / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / cell surface / endoplasmic reticulum / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Voltage gated sodium channel, alpha-5 subunit / 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 / Voltage-dependent channel domain superfamily / EF-hand ...Voltage gated sodium channel, alpha-5 subunit / 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 / 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 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsChagot, B. / Potet, F. / Balser, J.R. / Chazin, W.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Solution NMR Structure of the C-terminal EF-hand Domain of Human Cardiac Sodium Channel NaV1.5.
Authors: Chagot, B. / Potet, F. / Balser, J.R. / Chazin, W.J.
History
DepositionNov 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: 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_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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium channel protein type 5 subunit alpha


Theoretical massNumber of molelcules
Total (without water)10,9941
Polymers10,9941
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sodium channel protein type 5 subunit alpha / / Sodium channel protein type V subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.5 / ...Sodium channel protein type V subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.5 / Sodium channel protein cardiac muscle subunit alpha / HH1


Mass: 10994.207 Da / Num. of mol.: 1 / Fragment: EF-Hand domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: pET27 derivative / Gene: SCN5A / Plasmid: pBG100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14524

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D (H)CCH-COSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11022D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] entity, 100% H2O100% H2O
21.2 mM entity, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity[U-100% 13C; U-100% 15N]1
1.2 mMentity2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospinprocessing
TopSpin2Bruker Biospincollection
CYANA2.1Guntert, P. et al.structure solution
Amber9Case, D. et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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