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- PDB-2ndj: Structural Basis for KCNE3 and Estrogen Modulation of the KCNQ1 C... -

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Basic information

Entry
Database: PDB / ID: 2ndj
TitleStructural Basis for KCNE3 and Estrogen Modulation of the KCNQ1 Channel
ComponentsPotassium voltage-gated channel subfamily E member 3
KeywordsMEMBRANE PROTEIN / Estrogen / Ion channel
Function / homology
Function and homology information


negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of potassium ion export across plasma membrane / basolateral part of cell / negative regulation of voltage-gated potassium channel activity / Phase 3 - rapid repolarisation / membrane repolarization during action potential / membrane repolarization during ventricular cardiac muscle cell action potential / Phase 2 - plateau phase / potassium ion export across plasma membrane / intracellular chloride ion homeostasis ...negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of potassium ion export across plasma membrane / basolateral part of cell / negative regulation of voltage-gated potassium channel activity / Phase 3 - rapid repolarisation / membrane repolarization during action potential / membrane repolarization during ventricular cardiac muscle cell action potential / Phase 2 - plateau phase / potassium ion export across plasma membrane / intracellular chloride ion homeostasis / negative regulation of delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / monoatomic ion channel complex / neuronal cell body membrane / sodium ion transport / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel regulator activity / perikaryon / vesicle / transmembrane transporter binding / membrane raft / dendrite / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNE3 / Potassium channel, voltage-dependent, beta subunit, KCNE / Slow voltage-gated potassium channel
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily E member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailsclosest to the average, model3
AuthorsSanders, C.R. / Van Horn, W.D. / Kroncke, B.M. / Sisco, N.J. / Meiler, J. / Vanoye, C.G. / Song, Y. / Nannemann, D.P. / Welch, R.C. / Kang, C. ...Sanders, C.R. / Van Horn, W.D. / Kroncke, B.M. / Sisco, N.J. / Meiler, J. / Vanoye, C.G. / Song, Y. / Nannemann, D.P. / Welch, R.C. / Kang, C. / Smith, J. / George, A.L.
CitationJournal: Sci Adv / Year: 2016
Title: Structural basis for KCNE3 modulation of potassium recycling in epithelia.
Authors: Kroncke, B.M. / Van Horn, W.D. / Smith, J. / Kang, C. / Welch, R.C. / Song, Y. / Nannemann, D.P. / Taylor, K.C. / Sisco, N.J. / George, A.L. / Meiler, J. / Vanoye, C.G. / Sanders, C.R.
History
DepositionJun 9, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily E member 3


Theoretical massNumber of molelcules
Total (without water)12,8001
Polymers12,8001
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)10 / 9764structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Potassium voltage-gated channel subfamily E member 3 / MinK-related peptide 2 / Minimum potassium ion channel-related peptide 2 / Potassium channel ...MinK-related peptide 2 / Minimum potassium ion channel-related peptide 2 / Potassium channel subunit beta MiRP2


Mass: 12799.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNE3, MiRP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) RP Codon Plus / References: UniProt: Q9Y6H6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D HCACO
1812D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N; U-80% 2H]
Sample conditionspH: 6.5 / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxstructure solution
X-PLORSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
X-PLORSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 189 / NOE long range total count: 0 / NOE medium range total count: 79 / NOE sequential total count: 110 / Protein phi angle constraints total count: 98 / Protein psi angle constraints total count: 98
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 9764 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 5.544 ° / Torsion angle constraint violation method: Xplor-NIH, Amber

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