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- PDB-2h1z: Structure of a dual-target spider toxin -

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Basic information

Entry
Database: PDB / ID: 2h1z
TitleStructure of a dual-target spider toxin
ComponentsHybrid atracotoxin
KeywordsTOXIN / beta-hairpin / cystine knot
Biological speciesHadronyche versuta (spider)
MethodSOLUTION NMR / torsion angle dynamics (CYANA), simulated annealing (X-PLOR)
AuthorsSollod, B.L. / Maciejewski, M.W. / KIng, G.F.
Citation
Journal: To be Published
Title: A dual-target, self-synergizing toxin from spider venom
Authors: Sollod, B.L. / Gunning, S.J. / Maciejewski, M.W. / Nicholson, G.M. / King, G.F.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 1997
Title: The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider
Authors: Fletcher, J.I. / Smith, R. / O'Donoghue, S.I. / Nilges, M. / Connor, M. / Howden, M.E. / Christie, M.J. / King, G.F.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: Discovery and characterization of a family of insecticidal neurotoxins with a rare vicinal disulfide bridge
Authors: Wang, X.-H. / Connor, M. / Smith, R. / Maciejewski, M.W. / Howden, M.E. / Nicholson, G.M. / Christie, M.J. / KIng, G.F.
#3: Journal: Peptides / Year: 2005
Title: Were arachnids the first to use combinatorial peptide libraries?
Authors: Sollod, B.L. / Wilson, D. / Zhaxybayeva, O. / Gorgarten, J.P. / Drinkwater, R. / KIng, G.F.
History
DepositionMay 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hybrid atracotoxin


Theoretical massNumber of molelcules
Total (without water)4,2831
Polymers4,2831
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)25 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Hybrid atracotoxin


Mass: 4282.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadronyche versuta (spider) / Tissue: venom / Plasmid: pGEX-2T DERIVATIVE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
131HNHB
1423D 13C-separated NOESY
NMR detailsText: Dihedral-angle restraints were generated from TALOS analysis of chemical shift data.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C hybrid atracotoxin; 50 mM NaCl; 20 mM sodium phosphate, 90% H2O,10% D2O90% H2O/10% D2O
21 mM U-15N,13C hybrid atracotoxin; 50 mM NaCl; 20 mM sodium phosphate, 100% D2O100% D2O
Sample conditionsIonic strength: 50 mM NaCl, 20 mM NaPi / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A.processing
XEASYXia, T.-H. and Bartels, C.data analysis
CYANA1.1Guntert, P. and Herrman, T.structure solution
X-PLOR3.851Brunger, A.refinement
RefinementMethod: torsion angle dynamics (CYANA), simulated annealing (X-PLOR)
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 25

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