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- PDB-8fd4: Solution structure of mu-theraphotoxin Cg4a from Chinese tarantul... -

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Basic information

Entry
Database: PDB / ID: 8fd4
TitleSolution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
ComponentsJingzhaotoxin F7-10.36
KeywordsTOXIN / peptide / spider toxin / voltage-gated sodium channel modulator
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / toxin activity / extracellular region / Jingzhaotoxin F7-10.36
Function and homology information
Biological speciesChilobrachys guangxiensis (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSharma, G. / Jia, X. / Chin, Y.K.Y. / Mobli, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Solution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
Authors: Sharma, G. / Deuis, J. / Rahnama, S. / Jia, X. / Chin, Y.K.Y. / Undheim, E.A.B. / Vetter, I. / Mobli, M.
History
DepositionDec 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jingzhaotoxin F7-10.36


Theoretical massNumber of molelcules
Total (without water)3,9431
Polymers3,9431
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 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Jingzhaotoxin F7-10.36 / Peptide F7-10.36 / Mu-theraphotoxin Cg4a


Mass: 3942.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chilobrachys guangxiensis (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CH54
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-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
171isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
1101isotropic13D HNCO
1111isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 340 uM [U-100% 13C; U-100% 15N] Mu-theraphotoxin Cg4a, 20 mM sodium acetate, 5 % [U-2H] D2O, 95% H2O/5% D2O
Label: CN-Cg4a / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
340 uMMu-theraphotoxin Cg4a[U-100% 13C; U-100% 15N]1
20 mMsodium acetatenatural abundance1
5 %D2O[U-2H]1
Sample conditionsIonic strength: 20 mM / Label: condition1 / pH: 5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
TALOS-NProtein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks Y. Shen and A. Bax J Biomol NMR 2013 Vol. 56 Issue 3 Pages 227-41geometry optimization
TopSpinBruker Biospinprocessing
Rowland NMR Toolkit (RNMRTK)http://rnmrtk.uchc.edu/rnmrtk/RNMRTK. htmlprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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