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- PDB-9nvh: NMR structure of conotoxin k-SrXIA -

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Basic information

Entry
Database: PDB / ID: 9nvh
TitleNMR structure of conotoxin k-SrXIA
ComponentsKappa-conotoxin SrXIA
KeywordsTOXIN / Conotoxin / ion channel / Potassium
Function / homologyConotoxin I2-superfamily / I2-superfamily conotoxins / Conotoxin-I, conserved site / I-superfamily conotoxin signature. / potassium channel regulator activity / toxin activity / extracellular region / Kappa-conotoxin SrXIA
Function and homology information
Biological speciesConus spurius (invertebrata)
MethodSOLUTION NMR / molecular dynamics
AuthorsMelchor-Meneses, C.M. / del Rio-Portilla, F.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN214722 Mexico
CitationJournal: Toxicon / Year: 2025
Title: Block of Kv1 potassium channels and NMR structure of recombinant conotoxin kappa-SrXIA.
Authors: Escobar, L.I. / Quezada Suaste, C.D. / Salvador, C. / Aparicio, D.L. / Melchor-Meneses, C.M. / Bravo-Martinez, J. / de la Rosa, V. / Lopez-Gonzalez, Z. / Del Rio-Portilla, F.
History
DepositionMar 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-conotoxin SrXIA


Theoretical massNumber of molelcules
Total (without water)3,8651
Polymers3,8651
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kappa-conotoxin SrXIA / Kappa-SrXIA / I2-superfamily conotoxin sr11a


Mass: 3865.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus spurius (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0C615
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-TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM Conotoxin k-SrXIA, 95% H2O/5% D2O / Label: 1_Sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: Conotoxin k-SrXIA / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 1 mM / Label: Sample_1 / pH: 6 / 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: used also for simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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