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- PDB-2kyh: Solution structure of the voltage-sensing domain of KvAP -

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Basic information

Entry
Database: PDB / ID: 2kyh
TitleSolution structure of the voltage-sensing domain of KvAP
ComponentsVoltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


monoatomic ion channel complex / potassium channel activity / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Voltage-gated potassium channel
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsButterwick, J.A. / MacKinnon, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Solution Structure and Phospholipid Interactions of the Isolated Voltage-Sensor Domain from KvAP.
Authors: Butterwick, J.A. / Mackinnon, R.
History
DepositionMay 26, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_representative.selection_criteria / _struct.pdbx_model_details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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: Voltage-gated potassium channel


Theoretical massNumber of molelcules
Total (without water)16,1971
Polymers16,1971
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 #1minimized average structure

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Components

#1: Protein Voltage-gated potassium channel / / KvAP


Mass: 16197.295 Da / Num. of mol.: 1 / Fragment: UNP Residues 18-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE_0955 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YDF8
Sequence detailsPROCESSING BY THE E. COLI HOST HAS CHANGED THE FIRST FIVE RESIDUES (MET ALA ARG PHE ARG) TO LEU.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HNCA
1423D HN(CO)CA
1543D (H)CCH-COSY
1643D HN(COCA)CB
1743D 1H-15N NOESY
1843D 1H-13C NOESY
193TROSY HSQC
11033D 15N-edited NOESY
NMR detailsText: LOWEST ENERGY STRUCTURE IS MODEL 1. STRUCTURE CLOSEST TO THE MEAN COORDINATES IS MODEL 20.

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1-0.5 MM [U-98% 15N] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.1-0.5 MM [U-100% 13C U- 100% 15N U-80% 2H] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.1-0.5 MM [U-98% 13C U-98% 15N] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution40.1-0.5 MM [13CH3/12CD2]-LEU,VAL,[13CH3]-ILE ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2Osample_490% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity[U-98% 15N]0.1-0.51
20 mMHEPESnatural abundance1
20 mMpotassium chloridenatural abundance1
5 mMdiheptanoyl phosphatidylcholinenatural abundance1
mMentity[U-100% 13C; U-100% 15N; U-80% 2H]0.1-0.52
20 mMHEPESnatural abundance2
20 mMpotassium chloridenatural abundance2
5 mMdiheptanoyl phosphatidylcholinenatural abundance2
mMentity[U-100% 15N; U-80% 2H]0.1-0.53
20 mMHEPESnatural abundance3
20 mMpotassium chloridenatural abundance3
5 mMdiheptanoyl phosphatidylcholinenatural abundance3
mMentity[13CH3/12CD2]-Leu,Val,[13CH3]-Ile0.1-0.54
20 mMHEPESnatural abundance4
20 mMpotassium chloridenatural abundance4
5 mMdiheptanoyl phosphatidylcholinenatural abundance4
Sample conditionsIonic strength: 40 / pH: 7.0 / Pressure: AMBIENT / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX9001
Bruker DMXBrukerDMX8002
Bruker DMXBrukerDMX7003
Bruker DMXBrukerDMX6004

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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