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- PDB-2a9h: NMR structural studies of a potassium channel / charybdotoxin complex -

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Basic information

Entry
Database: PDB / ID: 2a9h
TitleNMR structural studies of a potassium channel / charybdotoxin complex
Components
  • Voltage-gated potassium channel
  • charybdotoxin
KeywordsMETAL TRANSPORT / membrane protein / Potassium channel / KcsA
Function / homology
Function and homology information


ion channel inhibitor activity / voltage-gated potassium channel activity / defense response to fungus / potassium channel regulator activity / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
pH-gated potassium channel KcsA / Potassium channel toxin alpha-KTx 1.1
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodSOLUTION NMR / molecular SIMULATED ANNEALING, dynamics, docking
Model type detailsminimized average
AuthorsYu, L. / Sun, C. / Song, D. / Shen, J. / Xu, N. / Gunasekera, A. / Hajduk, P.J. / Olejniczak, E.T.
CitationJournal: Biochemistry / Year: 2005
Title: Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex.
Authors: Yu, L. / Sun, C. / Song, D. / Shen, J. / Xu, N. / Gunasekera, A. / Hajduk, P.J. / Olejniczak, E.T.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_assembly ...entity_poly / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
E: charybdotoxin


Theoretical massNumber of molelcules
Total (without water)71,1805
Polymers71,1805
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein
Voltage-gated potassium channel


Mass: 16717.473 Da / Num. of mol.: 4 / Mutation: Q58A, T61S, R64D, F103Y, T107F, L110V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pIVEX-d2.4d / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: P0A334
#2: Protein/peptide charybdotoxin


Mass: 4309.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P13487*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-edited NOESY
1213D-filtered NOESY

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Sample preparation

DetailsContents: 1 mM KcsA, 2H and selectively 13C-methyl labeled in 20 mM sodium phosphate (pH 7.5), 5 mM KCl, 1 mM DTT, and 80 mM foscholine-12, 90% H2O/10% D2O or 100% D2O
Solvent system: 90% H2O/10% D2O or 100% D2O
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 315 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2002Brungerstructure solution
CNS2002Brungerrefinement
RefinementMethod: molecular SIMULATED ANNEALING, dynamics, docking / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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