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- PDB-2me7: NMR solution structure of the GS-TAMAPIN MUTATION R6A -

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Basic information

Entry
Database: PDB / ID: 2me7
TitleNMR solution structure of the GS-TAMAPIN MUTATION R6A
ComponentsPotassium channel toxin alpha-KTx 5.4
KeywordsTOXIN / Scorpion toxin / tamapin / alpha KTx5.4 mutant R6A
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 5.4
Function and homology information
Biological speciesMesobuthus tamulus (Indian red scorpion)
MethodSOLUTION NMR / molecular dynamics
Authorsdel Rio-Portilla, F. / Ramirez-Cordero, B.
CitationJournal: Chem.Res.Toxicol. / Year: 2014
Title: Cytotoxicity of recombinant tamapin and related toxin-like peptides on model cell lines.
Authors: Ramirez-Cordero, B. / Toledano, Y. / Cano-Sanchez, P. / Hernandez-Lopez, R. / Flores-Solis, D. / Saucedo-Yanez, A.L. / Chavez-Uribe, I. / Brieba, L.G. / Del Rio-Portilla, F.
History
DepositionSep 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 5.4


Theoretical massNumber of molelcules
Total (without water)3,5281
Polymers3,5281
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 5.4 / Tamapin


Mass: 3528.199 Da / Num. of mol.: 1 / Mutation: R8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus tamulus (Indian red scorpion)
Plasmid: modified pEt32a / Production host: Escherichia coli (E. coli) / References: UniProt: P59869

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY

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Sample preparation

DetailsContents: 3.0 mM toxin, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 3.0 mM / Component: toxin-1
Sample conditionspH: 3.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: AMBER / Version: 99
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 458 / NOE long range total count: 85 / NOE medium range total count: 83
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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