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- PDB-2m36: Solution structure of the insecticidal spider-venom peptide Aps III -

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Basic information

Entry
Database: PDB / ID: 2m36
TitleSolution structure of the insecticidal spider-venom peptide Aps III
ComponentsU2-cyrtautoxin-As1a
KeywordsTOXIN / Asp III / mu-CUTX-As1a / inhibitor cystine knot / voltage-gated sodium channel / insect toxin
Function / homology
Function and homology information


envenomation resulting in negative regulation of high voltage-gated calcium channel activity in another organism / envenomation resulting in negative regulation of low voltage-gated calcium channel activity in another organism / envenomation resulting in modulation of transmission of nerve impulse in another organism / envenomation resulting in negative regulation of voltage-gated sodium channel activity in another organism / : / toxin activity / extracellular region
Similarity search - Function
Spider insecticidal peptide / Spider insecticidal peptide
Similarity search - Domain/homology
Biological speciesApomastus schlingeri (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsLowest MolProbity score, model 1
AuthorsKing, G.F. / Bende, N.S. / Mobli, M.
Citation
Journal: Biochem Pharmacol / Year: 2013
Title: The insecticidal neurotoxin Aps III is an atypical knottin peptide that potently blocks insect voltage-gated sodium channels.
Authors: Bende, N.S. / Kang, E. / Herzig, V. / Bosmans, F. / Nicholson, G.M. / Mobli, M. / King, G.F.
#1: Journal: Toxicon / Year: 1992
Title: Identification of insecticidal peptides from venom of the trap-door spider, Aptostichus schlingeri (Ctenizidae).
Authors: Skinner, W.S. / Dennis, P.A. / Li, J.P. / Quistad, G.B.
History
DepositionJan 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_status.status_code_nmr_data / _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: U2-cyrtautoxin-As1a


Theoretical massNumber of molelcules
Total (without water)3,8591
Polymers3,8591
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 scores
RepresentativeModel #1lowest molprobity score

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Components

#1: Protein/peptide U2-cyrtautoxin-As1a / U2-CUTX-As1a / Aptotoxin III / Aptotoxin-3 / Paralytic peptide III / PP III


Mass: 3859.333 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apomastus schlingeri (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P49268

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Aps III
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY aliphatic
1223D 1H-13C NOESY aromatic
1313D 1H-15N NOESY
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1914D HC(CO)NH
NMR detailsText: All NMR data except NOESY experiments were acquired using nonuniform sampling and transformed using MaxEnt.

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Sample preparation

Details
Solution-IDContentsSolvent system
1450 uM [U-100% 13C; U-100% 15N] As1a, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
2450 uM [U-100% 13C; U-100% 15N] As1a, 20 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMAs1a-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
450 uMAs1a-3[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-42
Sample conditionspH: 6.0 / 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
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthursecondary structure assignment
MolProbityDavis IW et al.analysis of stereochemical quality
TALOSCornilescu, Delaglio and Baxestimation of dihedral angles
Rowland_NMR_ToolkitHoch, Stern et al.nmr data transformation
CYANAHoch, Stern et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 547 / NOE intraresidue total count: 117 / NOE long range total count: 171 / NOE medium range total count: 92 / NOE sequential total count: 167 / Disulfide bond constraints total count: 12 / Hydrogen bond constraints total count: 12
NMR representativeSelection criteria: lowest molprobity score
NMR ensembleConformer selection criteria: Best MolProbity scores / Conformers calculated total number: 200 / Conformers submitted total number: 20

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