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- PDB-6d8q: NMR solution structure of tamapin, mutant DP30/Y31+N -

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Basic information

Entry
Database: PDB / ID: 6d8q
TitleNMR solution structure of tamapin, mutant DP30/Y31+N
ComponentsPotassium channel toxin alpha-KTx 5.4
KeywordsTOXIN / Tamapin mutant / DP30/Y31+N / CSalpha/beta / SK channels
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. / Melchor Meneses, C.M. / Titaux Delgado, G.A. / Mayorga Flores, M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Novel Blocker of Onco SK3 Channels Derived from Scorpion Toxin Tamapin and Active against Migration of Cancer Cells
Authors: Flores, M. / Chantome, A. / Melchor-Meneses, C.M. / Domingo, I. / Titaux Delgado, G.A. / Galindo-Murillo, R. / Vandier, C. / del Rio Portilla, F.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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)3,4871
Polymers3,4871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3487.174 Da / Num. of mol.: 1 / Mutation: P30Y, Y31N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus tamulus (Indian red scorpion)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P59869
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 2.0 mM Potassium channel toxin alpha-KTx 5.4, 95% H2O/5% D2O
Label: 1H_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 2.0 mM / Component: Potassium channel toxin alpha-KTx 5.4 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichpeak picking
NMRPipe2014Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: used also for simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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