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- PDB-9ebe: Solution structure of sigma-S-GVIIIA conotoxin extracted from Con... -

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Basic information

Entry
Database: PDB / ID: 9ebe
TitleSolution structure of sigma-S-GVIIIA conotoxin extracted from Conus geographus
ComponentsSigma-conotoxin GVIIIA
KeywordsNEUROPEPTIDE / GFCK / 5-HT3 antagonist / cysteine-rich peptide
Function / homologyion channel regulator activity / toxin activity / extracellular region / Sigma-conotoxin GVIIIA
Function and homology information
Biological speciesConus geographus (geography cone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPeck, Y. / Daly, N.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2025
Title: Structural characterisation of a cysteine-rich conotoxin, sigma( sigma )S-GVIIIA, extracted from the defensive venom of the marine cone snail Conus geographus.
Authors: Peck, Y. / Wilson, D. / Lennox-Bulow, D. / Giribaldi, J. / Seymour, J. / Dutertre, S. / Rosengren, K. / Liddell, M. / Daly, N.
History
DepositionNov 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma-conotoxin GVIIIA


Theoretical massNumber of molelcules
Total (without water)4,2071
Polymers4,2071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Sigma-conotoxin GVIIIA


Mass: 4206.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus geographus (geography cone) / References: UniProt: P58924
Has ligand of interestN
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
111anisotropic22D 1H-1H NOESY
121anisotropic22D 1H-1H TOCSY
131anisotropic22D 1H-1H COSY
141anisotropic22D 1H-13C HSQC
151anisotropic21D

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Sample preparation

DetailsType: solution / Contents: 0.26 mM Sigma-S-GVIIIA conotoxin, 90% H2O/10% D2O / Label: GVIIIA / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.26 mM / Component: Sigma-S-GVIIIA conotoxin / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: 298K / pH: 4 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO9001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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