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- PDB-8cjr: JzTx-34 toxin peptide W25A mutant -

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Basic information

Entry
Database: PDB / ID: 8cjr
TitleJzTx-34 toxin peptide W25A mutant
ComponentsMu-theraphotoxin-Cg1a
KeywordsTOXIN / JZTX-34 PEPTIDE TOXIN / hNav1.1 channel sodium channel
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region / Mu-theraphotoxin-Cg1a
Function and homology information
Biological speciesChilobrachys (spider)
MethodSOLUTION NMR / molecular dynamics
AuthorsLandon, C. / Meudal, H.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Biomed Pharmacother / Year: 2023
Title: Structure-function relationship of new peptides activating human Na v 1.1.
Authors: Lopez, L. / De Waard, S. / Meudal, H. / Caumes, C. / Khakh, K. / Peigneur, S. / Oliveira-Mendes, B. / Lin, S. / De Waele, J. / Montnach, J. / Cestele, S. / Tessier, A. / Johnson, J.P. / ...Authors: Lopez, L. / De Waard, S. / Meudal, H. / Caumes, C. / Khakh, K. / Peigneur, S. / Oliveira-Mendes, B. / Lin, S. / De Waele, J. / Montnach, J. / Cestele, S. / Tessier, A. / Johnson, J.P. / Mantegazza, M. / Tytgat, J. / Cohen, C. / Beroud, R. / Bosmans, F. / Landon, C. / De Waard, M.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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
C: Mu-theraphotoxin-Cg1a


Theoretical massNumber of molelcules
Total (without water)4,0491
Polymers4,0491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mu-theraphotoxin-Cg1a / Mu-TRTX-Cg1a / Jingzhaotoxin-34 / JZTX-34 / Peptide F6-25.51


Mass: 4048.676 Da / Num. of mol.: 1 / Mutation: W25A / Source method: obtained synthetically / Source: (synth.) Chilobrachys (spider) / References: UniProt: B1P1F7
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
111anisotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-1H COSY
141anisotropic12D 1H-15N HSQC
151anisotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.1 mM unlabelled JzTx-34 W25A mutant (Jingzhaotoxin-34), 90% H2O/10% D2O
Label: unlabelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.1 mM / Component: JzTx-34 W25A mutant (Jingzhaotoxin-34) / Isotopic labeling: unlabelled
Sample conditionsIonic strength: 0 Not defined / Label: unlabelled / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNpeak 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: 250 / Conformers submitted total number: 10

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