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- PDB-8bwb: Spider toxin Pha1b (PnTx3-6) from Phoneutria nigriventer targetin... -

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Basic information

Entry
Database: PDB / ID: 8bwb
TitleSpider toxin Pha1b (PnTx3-6) from Phoneutria nigriventer targeting CaV2.x calcium channels and TRPA1 channel
ComponentsOmega-ctenitoxin-Pn4a
KeywordsTOXIN / spider toxin / neurotoxin / cystine-knot peptide / antagonist of CaV2.x calcium channels and TRPA1 channel
Function / homologycalcium channel regulator activity / toxin activity / extracellular region / Omega-ctenitoxin-Pn4a
Function and homology information
Biological speciesPhoneutria nigriventer (Brazilian armed spider)
MethodSOLUTION NMR / distance geometry
AuthorsMironov, P.A. / Chernaya, E.M. / Paramonov, A.S. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation22-14-00326 Russian Federation
CitationJournal: Toxins / Year: 2023
Title: Recombinant Production, NMR Solution Structure, and Membrane Interaction of the Ph alpha 1 beta Toxin, a TRPA1 Modulator from the Brazilian Armed Spider Phoneutria nigriventer .
Authors: Lyukmanova, E.N. / Mironov, P.A. / Kulbatskii, D.S. / Shulepko, M.A. / Paramonov, A.S. / Chernaya, E.M. / Logashina, Y.A. / Andreev, Y.A. / Kirpichnikov, M.P. / Shenkarev, Z.O.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Omega-ctenitoxin-Pn4a


Theoretical massNumber of molelcules
Total (without water)6,0551
Polymers6,0551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Omega-ctenitoxin-Pn4a / Omega-CNTX-Pn4a / CTK 01512-2 / Neurotoxin Tx3-6 / PnTx3-6 / Ph-alpha-1-beta toxin


Mass: 6055.089 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phoneutria nigriventer (Brazilian armed spider)
Plasmid: pET-32a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P81792

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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 TOCSY
131isotropic12D 1H-13C HSQC
142isotropic13D 1H-15N NOESY
152isotropic13D 1H-15N TOCSY
162isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.7 mM Pha1b, 5 % [U-99% 2H] D2O, 95% H2O/5% D2Onatural abundance95% H2O/5% D2O
solution22.7 mM [U-100% 15N] Pha1b, 5 % [U-99% 2H] D2O, 20 uM sodium acetate, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMPha1bnatural abundance1
5 %D2O[U-99% 2H]1
2.7 mMPha1b[U-100% 15N]2
5 %D2O[U-99% 2H]2
20 uMsodium acetatenatural abundance2
Sample conditionsIonic strength: 1 mM / Label: condition_1 / pH: 4.5 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichpeak picking
TopSpin4.0.7Bruker Biospinprocessing
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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