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- PDB-8pwt: Solution structure of the peptide U11-MYRTX-Tb1a from the venom o... -

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Basic information

Entry
Database: PDB / ID: 8pwt
TitleSolution structure of the peptide U11-MYRTX-Tb1a from the venom of the ant Tetramorium bicarinatum
ComponentsU11-myrmicitoxin-Tb1a
KeywordsTOXIN / ant venom peptide / neurotoxin / Tetramorium / helix peptide
Function / homologypotassium channel regulator activity / toxin activity / extracellular region / U11-myrmicitoxin-Tb1a
Function and homology information
Biological speciesTetramorium bicarinatum (insect)
MethodSOLUTION NMR / simulated annealing
AuthorsJouvensal, L. / Paquet, F. / Loth, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Toxins / Year: 2023
Title: Discovery of an Insect Neuroactive Helix Ring Peptide from Ant Venom.
Authors: Barasse, V. / Jouvensal, L. / Boy, G. / Billet, A. / Ascoet, S. / Lefranc, B. / Leprince, J. / Dejean, A. / Lacotte, V. / Rahioui, I. / Sivignon, C. / Gaget, K. / Ribeiro Lopes, M. / ...Authors: Barasse, V. / Jouvensal, L. / Boy, G. / Billet, A. / Ascoet, S. / Lefranc, B. / Leprince, J. / Dejean, A. / Lacotte, V. / Rahioui, I. / Sivignon, C. / Gaget, K. / Ribeiro Lopes, M. / Calevro, F. / Da Silva, P. / Loth, K. / Paquet, F. / Treilhou, M. / Bonnafe, E. / Touchard, A.
History
DepositionJul 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: U11-myrmicitoxin-Tb1a


Theoretical massNumber of molelcules
Total (without water)4,0341
Polymers4,0341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide U11-myrmicitoxin-Tb1a / U11-MYRTX-Tb1a


Mass: 4033.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetramorium bicarinatum (insect) / References: UniProt: A0A6M3Z554
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
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1.9 mM U11, 90% H2O/10% D2O / Label: U11 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.9 mM / Component: U11 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 5.1 / 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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 15

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