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- PDB-7lgl: Structural characterization of two b-KTx scorpion toxins. One of ... -

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Basic information

Entry
Database: PDB / ID: 7lgl
TitleStructural characterization of two b-KTx scorpion toxins. One of them blocks human KCNQ1 potassium channels
ComponentsPotassium channel toxin TcoKIK
KeywordsTOXIN / B-KTx / NMR solution structure / scorpion toxins / cysteine-stabilized ab motif / TcoKIK / Beta-KTx14.3 / KCNQ1 / Kv7.1.
Function / homologyLong chain scorpion toxin family / Long chain scorpion toxin, cysteine-stabilized alpha/beta domain / BetaSPN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / other organism cell membrane / potassium channel regulator activity / toxin activity / extracellular region / membrane / Potassium channel toxin TcoKIK
Function and homology information
Biological speciesTityus costatus (scorpion)
MethodSOLUTION NMR / molecular dynamics
Authorsdel Rio-Portilla, F. / Lopez-Giraldo, A.E.
CitationJournal: To Be Published
Title: b-KTx scorpion toxin blocks human KCNQ1 potassium channels
Authors: del Rio-Portilla, F. / Lopez-Giraldo, A.E.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 30, 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 TcoKIK


Theoretical massNumber of molelcules
Total (without water)5,2941
Polymers5,2941
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 TcoKIK


Mass: 5294.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tityus costatus (scorpion) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q0GY42
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 NOESY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.2 mM TcoKIK, 95% H2O/5% D2O / Label: 1H_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.2 mM / Component: TcoKIK / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / 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
CARA1.5Keller and Wuthrichchemical shift assignment
CARA1.5Keller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
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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