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- PDB-2l0w: Solution NMR structure of the N-terminal PAS domain of HERG potas... -

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Basic information

Entry
Database: PDB / ID: 2l0w
TitleSolution NMR structure of the N-terminal PAS domain of HERG potassium channel
ComponentsPotassium voltage-gated channel, subfamily H (Eag-related), member 2, isoform CRA_bVoltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / hERG / PAS Domain / Voltage-gated Potassium Channel
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 / cellular response to xenobiotic stimulus => GO:0071466 / 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 ...inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / cellular response to xenobiotic stimulus => GO:0071466 / 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 / plasma membrane => GO:0005886 / 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) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...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) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 2 / Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, Generalised Born Energy Minimization, GENERALISED BORN ENERGY MINIMIZATION WITH NMR RESTRAINTS
Model detailslowest energy, model 1
AuthorsNg, C.A. / Hunter, M.J. / Mobli, M. / King, G.F. / Kuchel, P.W. / Vandenberg, J.I.
CitationJournal: PLoS ONE / Year: 2011
Title: The N-Terminal Tail of hERG Contains an Amphipathic alpha-Helix That Regulates Channel Deactivation
Authors: Ng, C.A. / Hunter, M.J. / Perry, M.D. / Mobli, M. / Ke, Y. / Kuchel, P.W. / King, G.F. / Stock, D. / Vandenberg, J.I.
History
DepositionJul 19, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: 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: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel, subfamily H (Eag-related), member 2, isoform CRA_b


Theoretical massNumber of molelcules
Total (without water)15,5001
Polymers15,5001
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 Potassium voltage-gated channel, subfamily H (Eag-related), member 2, isoform CRA_b / Voltage-gated potassium channel


Mass: 15499.996 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 1-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: TEV cleavage site / Gene: KCNH2, hCG_18699 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: D3DX04, UniProt: Q12809*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY
1213D 1H-15N NOESY
1312D 1H-15N HSQC
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1813D HNCO
1913D HNCA
11013D HN(CO)CA
11113D HNCA
11223D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1150 mM sodium chloride-1, 10 mM HEPES-2, 3 mM TCEP-3, 7 % [U-100% 2H] D2O-4, 5 mM Octyl Glucoside-5, 93 % H2O-6, 99 % [U-99% 15N] N15 labeled PAS-7, 93% H2O/7% D2O93% H2O/7% D2O
2150 mM sodium chloride-8, 10 mM HEPES-9, 3 mM TCEP-10, 100 % [U-100% 2H] D2O-11, 5 mM Octyl Glucoside-12, 99 % [U-99% 13C; U-99% 15N] N15/C13 labeled PAS-13, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium chloride-11
10 mMHEPES-21
3 mMTCEP-31
7 %D2O-4[U-100% 2H]1
5 mMOctyl Glucoside-51
93 %H2O-61
99 %N15 labeled PAS-7[U-99% 15N]1
150 mMsodium chloride-82
10 mMHEPES-92
3 mMTCEP-102
100 %D2O-11[U-100% 2H]2
5 mMOctyl Glucoside-122
99 %N15/C13 labeled PAS-13[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 150mM / pH: 6.9 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: BRUKER Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
TALOSCornilescu, Delaglio and Baxdihedral angles calculation
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
RefinementMethod: DGSA-distance geometry simulated annealing, Generalised Born Energy Minimization, GENERALISED BORN ENERGY MINIMIZATION WITH NMR RESTRAINTS
Software ordinal: 1
Details: CYANA 2.1, AMBER 10 with NMR restraints, FORMATION 3 ENERGY 0.0000
NMR constraintsNOE constraints total: 2634 / NOE long range total count: 877 / NOE medium range total count: 498 / NOE sequential total count: 1259 / Hydrogen bond constraints total count: 96
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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