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- PDB-6mzt: Solution structure of alpha-KTx-6.21 (UroTx) from Urodacus yaschenkoi -

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Basic information

Entry
Database: PDB / ID: 6mzt
TitleSolution structure of alpha-KTx-6.21 (UroTx) from Urodacus yaschenkoi
ComponentsPotassium channel toxin alpha-KTx 6.21
KeywordsTOXIN / Scopion toxin / Cysteine-stabilized alpha-beta motif
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 6.21
Function and homology information
Biological speciesUrodacus yaschenkoi (scorpion)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Luna-Ramirez, K. / Anangi, R. / King, G.F.
CitationJournal: Biochem. Pharmacol. / Year: 2020
Title: Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom.
Authors: Luna-Ramirez, K. / Csoti, A. / McArthur, J.R. / Chin, Y.K.Y. / Anangi, R. / Najera, R.D.C. / Possani, L.D. / King, G.F. / Panyi, G. / Yu, H. / Adams, D.J. / Finol-Urdaneta, R.K.
History
DepositionNov 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Oct 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 6.21


Theoretical massNumber of molelcules
Total (without water)4,0291
Polymers4,0291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2930 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy and the best stereochemical properties
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 6.21 / Urotoxin


Mass: 4028.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Urodacus yaschenkoi (scorpion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0DL37
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-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] UroTx, 20 mM sodium acetate, 5 % D2O, 95% H2O/5% D2O
Label: Sample 1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMUroTx[U-13C; U-15N]1
20 mMsodium acetatenatural abundance1
5 %D2Onatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: condition1 / pH: 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: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
TALOS-NCornilescu, Delaglio and Baxgeometry optimization
Rowland NMR Toolkithttp://www.rowland.org/rnmrtk/toolkit.htmlprocessing
AnalysisCCPNdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and the best stereochemical properties
Conformers calculated total number: 30 / Conformers submitted total number: 20

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