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- PDB-2n1n: Solution structure of VSTx1 -

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Basic information

Entry
Database: PDB / ID: 2n1n
TitleSolution structure of VSTx1
ComponentsKappa-theraphotoxin-Gr3a
KeywordsTOXIN
Function / homology
Function and homology information


ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Kappa-theraphotoxin-Gr3a
Similarity search - Component
Biological speciesGrammostola rosea (Chilean rose tarantula)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLau, H.Y. / King, G.F. / Mobli, M.
CitationJournal: Sci Rep
Title: Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels.
Authors: Lau, C.H. / King, G.F. / Mobli, M.
History
DepositionApr 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-theraphotoxin-Gr3a


Theoretical massNumber of molelcules
Total (without water)4,0971
Polymers4,0971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kappa-theraphotoxin-Gr3a / Kappa-TRTX-Gr3a / Voltage sensor toxin 1 / VsTx1


Mass: 4096.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grammostola rosea (Chilean rose tarantula)
Production host: Escherichia coli (E. coli) / References: UniProt: P60980
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D 1H-15N NOESY
1612D 1H-13C HSQC aliphatic
1712D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 20 mM sodium acetate, 1.7 mM [U-99% 13C; U-99% 15N] VSTx1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetate-11
1.7 mMVSTx1-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.peak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
Rowland_NMR_Toolkit3Jeffrey C. Hoch and Alan S. Sternprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Simulated annealing, with automated NOE assignment
NMR constraintsNOE constraints total: 694 / NOE intraresidue total count: 193 / NOE long range total count: 179 / NOE medium range total count: 116 / NOE sequential total count: 206 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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