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- PDB-2mi5: Structure of insect-specific sodium channel toxin mu-Dc1a -

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Basic information

Entry
Database: PDB / ID: 2mi5
TitleStructure of insect-specific sodium channel toxin mu-Dc1a
ComponentsMu-diguetoxin-Dc1a
KeywordsTOXIN / spider venom / insecticidal toxin / sodium channel / voltage-sensor / gating modifier / non-uniform sampling / DTX9.2 / inhibitor cystine knot / knottin
Function / homology
Function and homology information


host cell presynaptic membrane / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #120 / Beta/Mu-diguetoxin-1 / Spider Toxins mu-diguetoxin-1 a, b and c / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / Mainly Beta
Similarity search - Domain/homology
Beta-diguetoxin-Dc1a
Similarity search - Component
Biological speciesDiguetia canities (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsBest MolProbity score, model1
AuthorsBende, N.S. / Mobli, M. / King, G.F.
Citation
Journal: Nat Commun / Year: 2014
Title: A distinct sodium channel voltage-sensor locus determines insect selectivity of the spider toxin Dc1a.
Authors: Bende, N.S. / Dziemborowicz, S. / Mobli, M. / Herzig, V. / Gilchrist, J. / Wagner, J. / Nicholson, G.M. / King, G.F. / Bosmans, F.
#1: Journal: Insect Biochem.Mol.Biol. / Year: 1995
Title: Characterization and cloning of insecticidal peptides from the primitive weaving spider Diguetia canities.
Authors: Krapcho, K.J. / Kral, R.M. / Vanwagenen, B.C. / Eppler, K.G. / Morgan, T.K.
#2: Journal: Toxicon / Year: 1996
Title: Mode of action of an insecticidal peptide toxin from the venom of a weaving spider (Diguetia canities).
Authors: Bloomquist, J.R. / Kinne, L.P. / Deutsch, V. / Simpson, S.F.
History
DepositionDec 8, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 20, 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
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu-diguetoxin-Dc1a


Theoretical massNumber of molelcules
Total (without water)6,5021
Polymers6,5021
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 / 200Best MolProbity score
RepresentativeModel #1best molprobity score

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Components

#1: Protein Mu-diguetoxin-Dc1a / Mu-DGTX-Dc1a / Insecticidal toxin DTX9.2


Mass: 6502.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diguetia canities (spider) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49126
Has protein modificationY
Sequence detailsVESTIGE OF PROTEASE RECOGNITION SITE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D CBCA(CO)NH
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D 1H-15N NOESY
11014D HCC(CO)NH
NMR detailsText: All 3D and 4D except NOESY type data were acquired using non-uniform sampling and processed using maximum entropy.

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Sample preparation

DetailsContents: 350 uM [U-99% 13C; U-99% 15N] Dc1a-1, 20 mM sodium acetate-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMDc1a-1[U-99% 13C; U-99% 15N]1
20 mMsodium acetate-21
Sample conditionsIonic strength: 0.02 / 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
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
XEASYBartels et al.chemical shift assignment
TopSpin3Bruker Biospincollection
Rowland_NMR_Toolkit3Jeffrey C. Hoch, Alan S. Sternprocessing
GENPROC2Mehdi Mobliprocessing
CYANA3refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 902 / NOE intraresidue total count: 267 / NOE long range total count: 276 / NOE medium range total count: 106 / NOE sequential total count: 253
NMR representativeSelection criteria: best molprobity score
NMR ensembleConformer selection criteria: Best MolProbity score / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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