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- PDB-7l83: NMR solution structure of Nav1.5 DIV S3b-S4a paddle motif in DPC ... -

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Basic information

Entry
Database: PDB / ID: 7l83
TitleNMR solution structure of Nav1.5 DIV S3b-S4a paddle motif in DPC micelle
ComponentsSodium channel protein type 5 subunit alpha
KeywordsMEMBRANE PROTEIN / Sodium channel / voltage sensing
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 Purkinje myocyte 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 / 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 Purkinje myocyte 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 / response to denervation involved in regulation of muscle adaptation / membrane depolarization during atrial cardiac muscle cell action potential / cardiac ventricle development / regulation of atrial cardiac muscle cell membrane repolarization / regulation of ventricular cardiac muscle cell membrane depolarization / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / brainstem development / membrane depolarization during AV node cell action potential / positive regulation of action potential / membrane depolarization during bundle of His cell action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction system development / telencephalon development / regulation of sodium ion transmembrane transport / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / Interaction between L1 and Ankyrins / ankyrin binding / voltage-gated sodium channel activity / sodium ion transport / nitric-oxide synthase binding / Phase 0 - rapid depolarisation / fibroblast growth factor binding / odontogenesis of dentin-containing tooth / regulation of heart rate by cardiac conduction / membrane depolarization / intercalated disc / lateral plasma membrane / cardiac muscle contraction / T-tubule / sodium ion transmembrane transport / cerebellum development / regulation of heart rate / cellular response to calcium ion / positive regulation of epithelial cell proliferation / sarcolemma / caveola / Z disc / scaffold protein binding / transmembrane transporter binding / calmodulin binding / protein domain specific binding / ubiquitin protein ligase binding / protein kinase binding / nucleolus / 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 / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily ...Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHussein, A.K. / Bhuiyan, M.H. / Arshava, B. / Zhuang, J. / Poget, S.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM124606-01 United States
National Science Foundation (NSF, United States)MCB-1253277 United States
CitationJournal: Biorxiv / Year: 2021
Title: NMR solution structure and analysis of isolated S3b-S4a motif of repeat IV of the human cardiac sodium channel
Authors: Hussein, A.K. / Bhuiyan, M.H. / Arshava, B. / Zhuang, J. / Poget, S.F.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)4,2091
Polymers4,2091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Sodium channel protein type 5 subunit alpha / Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit alpha / ...Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.5 / hH1


Mass: 4209.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN5A / Production host: Escherichia coli (E. coli) / References: UniProt: Q14524

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
222isotropic13D HN(CA)CB
232isotropic13D 1H-15N NOESY
141isotropic13D (H)CCH-TOCSY
252isotropic23D HNCA

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15N] Nav1.5 DIV S3bS4a motif, 90% H2O/10% D2Opeptide paddle powder was dissolved in a buffer containing detergent micelle15N, 13C90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] Nav1.5 DIV S3bS4a motif, 90% H2O/10% D2Opeptide paddle powder was dissolved in a buffer containing detergent micellesample_190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNav1.5 DIV S3bS4a motif[U-13C; U-15N]1
0.5 mMNav1.5 DIV S3bS4a motif[U-13C; U-15N]2
Sample conditions

Ionic strength: 10 Nacl, 10 potassium phosphate mM / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Temperature: 310 K

Conditions-IDDetailsLabel
1Nav.15 DIV S3bS4a was dissolved in 10 mM NaCl, 10 mM potassium phosphate, pH 7.0 100 mM n-dodecylphosphocholine (DPC) in 100 % D20100% D20
2Nav.15 DIV S3bS4a was dissolved in 10 mM NaCl, 10 mM potassium phosphate, pH 7.0 100 mM n-dodecylphosphocholine (DPC) in 10% D20, 90% H2010% D20

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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