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- PDB-2m50: Analysis of the structural and molecular basis of voltage-sensiti... -

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Basic information

Entry
Database: PDB / ID: 2m50
TitleAnalysis of the structural and molecular basis of voltage-sensitive sodium channel inhibition by the spider toxin, Huwentoxin-IV (-TRTX-Hh2a).
ComponentsMu-theraphotoxin-Hh2a
KeywordsTOXIN / venom toxin
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsGibbs, A. / Minassian, N. / Flinspach, M. / Wickenden, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Analysis of the Structural and Molecular Basis of Voltage-sensitive Sodium Channel Inhibition by the Spider Toxin Huwentoxin-IV ( mu-TRTX-Hh2a).
Authors: Minassian, N.A. / Gibbs, A. / Shih, A.Y. / Liu, Y. / Neff, R.A. / Sutton, S.W. / Mirzadegan, T. / Connor, J. / Fellows, R. / Husovsky, M. / Nelson, S. / Hunter, M.J. / Flinspach, M. / Wickenden, A.D.
History
DepositionFeb 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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_database_related.db_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: Mu-theraphotoxin-Hh2a


Theoretical massNumber of molelcules
Total (without water)4,0631
Polymers4,0631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mu-theraphotoxin-Hh2a / Mu-TRTX-Hh2a / Huwentoxin-4 / Huwentoxin-IV / HwTx-IV / Huwentoxin-IVa / HWTX-IVa / Huwentoxin-IVb ...Mu-TRTX-Hh2a / Huwentoxin-4 / Huwentoxin-IV / HwTx-IV / Huwentoxin-IVa / HWTX-IVa / Huwentoxin-IVb / HWTX-IVb / Huwentoxin-IVc / HWTX-IVc


Mass: 4062.762 Da / Num. of mol.: 1 / Fragment: unp residues 53-87 / Mutation: A82K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma schmidti (Chinese earth tiger)
Plasmid: pCDNA / Production host: Homo Sapiens (human) / References: UniProt: P83303

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: HWTX-IV(K32A)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 2 mM entity, 20 mM sodium phosphate, 150 uM sodium azide, 100 uM [U-99% 2H] EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-11
20 mMsodium phosphate-21
150 uMsodium azide-31
100 uMEDTA-4[U-99% 2H]1
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 950 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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