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- PDB-2n7g: Structure of the cyclic nucleotide-binding homology domain of the... -

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Basic information

Entry
Database: PDB / ID: 2n7g
TitleStructure of the cyclic nucleotide-binding homology domain of the hERG channel
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsMEMBRANE PROTEIN / hERG / CNBHD / ion channel / LQTS2
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 / Jelly Rolls / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLi, Y. / Ng, H. / Li, Q. / Kang, C.
CitationJournal: Sci Rep / Year: 2016
Title: Structure of the Cyclic Nucleotide-Binding Homology Domain of the hERG Channel and Its Insight into Type 2 Long QT Syndrome
Authors: Li, Y. / Ng, H.Q. / Li, Q. / Kang, C.
History
DepositionSep 10, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: 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_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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)17,4401
Polymers17,4401
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 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: 17439.932 Da / Num. of mol.: 1 / Fragment: UNP residues 734-869
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNH2, ERG, ERG1, HERG / Production host: Escherichia coli (E. coli) / Strain (production host): Roestta / References: UniProt: Q12809

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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 HN(CA)CB
1313D HN(COCA)CB
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D HN(CA)CO
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D H(CCO)NH
11113D 1H-15N NOESY
11212D 1H-13C HSQC
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] the cyclic nucleotide-binding homology domain of the hERG channel-1, 20 mM sodium phosphate-2, 150 mM sodium chloride-3, 1 mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMthe cyclic nucleotide-binding homology domain of the hERG channel-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-41
Sample conditionsIonic strength: 170 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipeBruker Biospinprocessing
NMRPipeBruker Biospinchemical shift assignment
NMRPipeBruker Biospinstructure solution
NMRPipeJohnson, One Moon Scientificprocessing
NMRPipeJohnson, One Moon Scientificchemical shift assignment
NMRPipeJohnson, One Moon Scientificstructure solution
NMRPipeKeller and Wuthrichprocessing
NMRPipeKeller and Wuthrichchemical shift assignment
NMRPipeKeller and Wuthrichstructure solution
NMRPipeGuntert, Mumenthaler and Wuthrichprocessing
NMRPipeGuntert, Mumenthaler and Wuthrichchemical shift assignment
NMRPipeGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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