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- PDB-2k21: NMR structure of human KCNE1 in LMPG micelles at pH 6.0 and 40 de... -

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Basic information

Entry
Database: PDB / ID: 2k21
TitleNMR structure of human KCNE1 in LMPG micelles at pH 6.0 and 40 degree C
ComponentsPotassium voltage-gated channel subfamily E member
KeywordsMEMBRANE PROTEIN / KCNE1 / potassium channel / MinK / auxilliary subunit / micelles / Ion transport / Ionic channel / Potassium transport / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


negative regulation of protein targeting to membrane / regulation of delayed rectifier 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 / telethonin binding / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity ...negative regulation of protein targeting to membrane / regulation of delayed rectifier 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 / telethonin binding / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity / membrane repolarization / delayed rectifier potassium channel activity / cardiac conduction / positive regulation of potassium ion transmembrane transport / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle cell action potential / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / cellular response to cAMP / potassium ion transmembrane transport / sensory perception of sound / Z disc / transmembrane transporter binding / lysosome / apical plasma membrane / membrane raft / cell surface / plasma membrane
Similarity search - Function
Potassium voltage-gated channel subfamily E member 1 / Potassium channel, voltage-dependent, beta subunit, KCNE / Slow voltage-gated potassium channel
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily E member 1 / KCNE1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsStructure of human KCNE1 (also known as MinK) in LMPG micelles. KCNE1 modulates certain voltage- ...Structure of human KCNE1 (also known as MinK) in LMPG micelles. KCNE1 modulates certain voltage-gated potassium channels.
AuthorsKang, C. / Tian, C. / Sonnichsen, F.D. / Smith, J.A. / Meiler, J. / George, A.L. / Vanoye, C.G. / Sanders, C.R. / Kim, H.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel.
Authors: Kang, C. / Tian, C. / Sonnichsen, F.D. / Smith, J.A. / Meiler, J. / George, A.L. / Vanoye, C.G. / Kim, H.J. / Sanders, C.R.
History
DepositionMar 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7071
Polymers15,7071
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 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Potassium voltage-gated channel subfamily E member


Mass: 15706.869 Da / Num. of mol.: 1 / Mutation: R104K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNE1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RP / References: UniProt: Q6FHJ6, UniProt: P15382*PLUS
Sequence detailsTHESE COORDINATES ARE FOR THE R104K MUTANT FORM OF KCNE1, WHICH WAS GENERATED AT AN EARLY STAGE IN ...THESE COORDINATES ARE FOR THE R104K MUTANT FORM OF KCNE1, WHICH WAS GENERATED AT AN EARLY STAGE IN STRUCTURAL DETERMINATION BY A PCR ERROR. THE R104K MUTANT MODULATES KCNQ1 CHANNEL FUNCTION IN WILD TYPE-LIKE MANNER. MUTATION OF THIS ARG RESIDUE TO LYS IS OBSERVED IN MAMMALIAN KCNE1 HOMOLOGS TO THE HUMAN PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TROSY-1H-15N HSQC
1223D TROSY-HNCO
1323D TROSY-HNCA
1423D TROSY-HN(CO)CA
1523D TROSY-CBCA(CO)NH
1623D TROSY-HN(CA)CB
1733D 1H-15N TROSY-NOESY
1842D TROSY-1H-15N HSQC
NMR detailsText: The structure was determined using combination of NOEs, PREs, and RDCs.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] KCNE1 (MinK), 10 % D2O, 2 mM EDTA, 2 mM DTT, 250 mM imidazole, 4 % LMPG, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N; U-2H] KCNE1 (MinK), 10 % D2O, 2 mM EDTA, 2 mM DTT, 250 mM imidazole, 4 % LMPG, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N; 70% 2H] KCNE1 (MinK), 10 % D2O, 2 mM EDTA, 2 mM DTT, 250 mM imidazole, 4 % LMPG, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-15N; U-2H] KCNE1 (MinK), 10 % D2O, 2 mM EDTA, 2 mM DTT, 250 mM imidazole, 4 % LMPG, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMKCNE1 (MinK)[U-100% 15N]1
10 %D2O1
2 mMEDTA1
2 mMDTT1
250 mMimidazole1
4 %LMPG1
1 mMKCNE1 (MinK)[U-13C; U-15N; U-2H]2
10 %D2O2
2 mMEDTA2
2 mMDTT2
250 mMimidazole2
4 %LMPG2
1 mMKCNE1 (MinK)[U-100% 13C; U-100% 15N; 70% 2H]3
10 %D2O3
2 mMEDTA3
2 mMDTT3
250 mMimidazole3
4 %LMPG3
1 mMKCNE1 (MinK)[U-15N; U-2H]4
10 %D2O4
2 mMEDTA4
2 mMDTT4
250 mMimidazole4
4 %LMPG4
Sample conditionsIonic strength: 0.25 / pH: 6.0 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
NMRPipev2.4Delaglio, F. et al.processing
NMRView5.2.2_01Johnson, B.A. et al.data analysis
CYANA2.1Guntert, P. et al.data analysis
X-PLOR NIH2.17Schwieters, C.D. et al.refinement
ProcheckNMRv.3.5.4Laskowski, R.A. et al.data analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: The refinement protocol consisted of slow cooling from 1000 K to 100 K spanning 45 ps. Final structures were energy-minimized using 250 steps of Powell energy minimization. The 20 structures ...Details: The refinement protocol consisted of slow cooling from 1000 K to 100 K spanning 45 ps. Final structures were energy-minimized using 250 steps of Powell energy minimization. The 20 structures with lowest energy were subjected to further analysis and spin-labeled Cys residues associated with PRE restraints were changed back to their wild type residues. Powell energy minimization was then performed.
NMR constraintsNOE constraints total: 737 / NOE intraresidue total count: 126 / NOE long range total count: 464 / NOE medium range total count: 50 / NOE sequential total count: 97 / Hydrogen bond constraints total count: 72 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 113 / Protein psi angle constraints total count: 112
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.2 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.137 Å / Maximum torsion angle constraint violation: 4.569 ° / Maximum upper distance constraint violation: 0.129 Å / Torsion angle constraint violation method: XPLOR
NMR ensemble rmsDistance rms dev: 0.008 Å / Distance rms dev error: 0.0019 Å

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