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- PDB-2le7: Solution nmr structure of the S4S5 linker of herg potassium channel -

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Basic information

Entry
Database: PDB / ID: 2le7
TitleSolution nmr structure of the S4S5 linker of herg potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsTRANSPORT PROTEIN / HERG / S4S5 / VOLTAGE-GATED POTASSIUM CHANNEL / MEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane depolarization during action potential / potassium ion export across plasma membrane ...inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane depolarization during action potential / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / C3HC4-type RING finger domain binding / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / membrane repolarization / regulation of membrane repolarization / delayed rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / Voltage gated Potassium channels / potassium ion homeostasis / ventricular cardiac muscle cell action potential / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / voltage-gated potassium channel complex / cardiac muscle contraction / potassium ion transmembrane transport / regulation of membrane potential / cellular response to xenobiotic stimulus / scaffold protein binding / transcription cis-regulatory region binding / ubiquitin protein ligase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / GENERALISED BORN ENERGY MINIMIZATION WITH NMR RESTRAINTS, DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsNg, C.A. / Kuchel, P.W. / Vandenberg, J.I.
CitationJournal: Plos One / Year: 2012
Title: The S4-S5 linker acts as a signal integrator for HERG K+ channel activation and deactivation gating
Authors: Ng, C.A. / Perry, M.D. / Tan, P.S. / Hill, A.P. / Kuchel, P.W. / Vandenberg, J.I.
History
DepositionJun 13, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily H member 2


Theoretical massNumber of molelcules
Total (without water)2,3311
Polymers2,3311
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium voltage-gated channel subfamily H member 2 / Eag homolog / Ether-a-go-go-related gene potassium channel 1 / ERG-1 / Eag-related protein 1 / ...Eag homolog / Ether-a-go-go-related gene potassium channel 1 / ERG-1 / Eag-related protein 1 / Ether-a-go-go-related protein 1 / H-ERG / hERG-1 / hERG1 / Voltage-gated potassium channel subunit Kv11.1


Mass: 2330.728 Da / Num. of mol.: 1 / Fragment: residues 532-551 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12809

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 100mM DPC-1, 90%(v/v) H2O-2, 10%(v/v) [U-2H] D2O-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMDPC-11
90 %H2O-21
10 %D2O-3[U-2H]1
Sample conditionspH: 6.6 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: BRUKER Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
CYANArefinement
RefinementMethod: GENERALISED BORN ENERGY MINIMIZATION WITH NMR RESTRAINTS, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR constraintsNOE constraints total: 271 / NOE long range total count: 25 / NOE medium range total count: 98 / NOE sequential total count: 148
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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