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- PDB-1hp3: C-TERMINAL TRUNCATION OF OMEGA-ATRACOTOXIN-HV2A (CT-HV2A) -

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Basic information

Entry
Database: PDB / ID: 1hp3
TitleC-TERMINAL TRUNCATION OF OMEGA-ATRACOTOXIN-HV2A (CT-HV2A)
ComponentsOMEGA-ATRACOTOXIN-HV2A
KeywordsTOXIN / Cystine knot
Function / homologyOmega-atracotoxin, conserved site-2 / Omega-atracotoxin (ACTX) type 2 family signature. / Magi 5 toxic peptide / Magi 5 toxic peptide family / sodium channel inhibitor activity / calcium channel inhibitor activity / toxin activity / extracellular region / Omega-hexatoxin-Hv2a
Function and homology information
MethodSOLUTION NMR / Torsion angle dynamics, dynamical simulated annealing
AuthorsWang, X.-H. / King, G.F.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Discovery and structure of a potent and highly specific blocker of insect calcium channels
Authors: Wang, X.-H. / Connor, M. / Wilson, D. / Wilson, H.I. / Nicholson, G.M. / Smith, R. / Shaw, D. / Mackay, J.P. / Alewood, P.F. / Christie, M.J. / King, G.F.
#1: Journal: Nat.Struct.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.H. / Nicholson, G.M.
#2: Journal: Nat.Struct.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.
History
DepositionDec 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 13, 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: OMEGA-ATRACOTOXIN-HV2A


Theoretical massNumber of molelcules
Total (without water)3,3841
Polymers3,3841
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide OMEGA-ATRACOTOXIN-HV2A / CT-HV2A


Mass: 3383.948 Da / Num. of mol.: 1 / Fragment: N-TERMINAL (RESIDUES 1-32) / Source method: obtained synthetically
Details: This sequence does not occur naturally. The peptide was chemically synthesized using standard t-Boc chemistry, and oxidized/folded in a glutathione redox buffer.
References: UniProt: P82852
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1322D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM CT-Hv2a95% H2O/5% D2O
22.5 mM CT-Hv2a100% D2O
Sample conditionsIonic strength: 0.005 / pH: 4.71 / Pressure: 1 atm / Temperature: 296 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
FelixFelix97Molecular Simulations, Inc.processing
X-EASY1.3.13Tai-he Xia & Christian Bartelsdata analysis
DYANA1.5Peter Guentertstructure solution
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: Torsion angle dynamics, dynamical simulated annealing
Software ordinal: 1
Details: The structures are based on a total of 345 NOE-derived distance restraints, 21 dihedral-angle restraints, plus 22 restraints defining 11 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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