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- PDB-1ujl: Solution Structure of the HERG K+ channel S5-P extracellular linker -

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Basic information

Entry
Database: PDB / ID: 1ujl
TitleSolution Structure of the HERG K+ channel S5-P extracellular linker
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsMEMBRANE PROTEIN / two helices / amphiphatic helix
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 / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / C3HC4-type RING finger domain binding / 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 / potassium ion transmembrane transport / cardiac muscle contraction / 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 / PAS domain / PAC domain profile. / 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 / PAS domain / PAC domain profile. / 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
MethodSOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
AuthorsTorres, A.M. / Bansal, P.S. / Sunde, M. / Clarke, C.E. / Bursill, J.A. / Smith, D.J. / Bauskin, A. / Breit, S.N. / Campbell, T.J. / Alewood, P.F. ...Torres, A.M. / Bansal, P.S. / Sunde, M. / Clarke, C.E. / Bursill, J.A. / Smith, D.J. / Bauskin, A. / Breit, S.N. / Campbell, T.J. / Alewood, P.F. / Kuchel, P.W. / Vandenberg, J.I.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of the HERG K+ channel S5P extracellular linker: role of an amphipathic alpha-helix in C-type inactivation.
Authors: Torres, A.M. / Bansal, P.S. / Sunde, M. / Clarke, C.E. / Bursill, J.A. / Smith, D.J. / Bauskin, A. / Breit, S.N. / Campbell, T.J. / Alewood, P.F. / Kuchel, P.W. / Vandenberg, J.I.
History
DepositionAug 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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
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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)4,5891
Polymers4,5891
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 / 1600structures with the lowest energy
RepresentativeModel #8used in the publication

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Components

#1: Protein/peptide Potassium voltage-gated channel subfamily H member 2 / HERG K+ channel S5-P extracellular linker / Ether-a-go-go related gene potassium channel 1 / H-ERG ...HERG K+ channel S5-P extracellular linker / Ether-a-go-go related gene potassium channel 1 / H-ERG / Erg1 / Ether-a-go-go related protein 1 / Eag related protein 1 / eag homolog


Mass: 4589.134 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-42 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q12809

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: The structures were determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1.4mM S5-P peptide / Solvent system: 100mM SDS, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0 / pH: 3.3 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerprocessing
XEASY1.3.13Bartels, C., Xia, T., Billeter, M., Guntert, P., Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
CNS1.1Brunger, A. T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
RefinementMethod: simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 430 restraints, 416 are NOE-derived distance constraints, 14 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: used in the publication
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1600 / Conformers submitted total number: 20

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