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- PDB-1i25: Three dimensional solution structure of huwentoxin-II by 2D 1H-NMR -

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Basic information

Entry
Database: PDB / ID: 1i25
TitleThree dimensional solution structure of huwentoxin-II by 2D 1H-NMR
ComponentsHUWENTOXIN-II
KeywordsTOXIN / neurotoxin / insecticidal toxin / disulfide bonds
Function / homologyHuwentoxin-II family / Huwentoxin-II family / Huwentoxin-2 family signature. / host cell postsynaptic membrane / : / toxin activity / extracellular region / U1-theraphotoxin-Hs1a
Function and homology information
Biological speciesOrnithoctonus huwena (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
AuthorsShu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
Citation
Journal: Protein Sci. / Year: 2002
Title: The structure of spider toxin huwentoxin-II with unique disulfide linkage: evidence for structural evolution.
Authors: Shu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
#1: Journal: ACTA BIOCHIM.BIOPHYS.SINICA / Year: 2001
Title: Sequence-specific Assignment of 1H-NMR Resonance and Determination of the Secondary Structure of HWTX-II
Authors: Shu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
#2: Journal: To be Published
Title: Assignment of Disulfide Bonds of Huwentoxin-II by Edman Degradation Sequencing and Stepwise Thiol Modification
Authors: Shu, Q. / Huang, R.H. / Liang, S.P.
#3: Journal: J.PEPT.RES. / Year: 1999
Title: Purification and Characterization of Huwentoxin-II, a Neurotoxic Peptide from the Venom of the Chinese Bird Spider Selenocosmia huwena
Authors: Shu, Q. / Liang, S.P.
History
DepositionFeb 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Remark 750TURN DETERMINATION METHOD: AUTHOR-DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUWENTOXIN-II


Theoretical massNumber of molelcules
Total (without water)4,3001
Polymers4,3001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide HUWENTOXIN-II / HWTX-II


Mass: 4300.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VENOM
Source: (natural) Ornithoctonus huwena (Chinese earth tiger)
Organ: VENOM GLAND / References: UniProt: P82959

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
142NOESY
152E-COSY
162TOCSY
271NOESY
281TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM Huwentoxin-II; 20 mmol/l phosphate buffer; 90%H2O , 10%D2O90% H2O/10% D2O
24 mM Huwentoxin-II; 20 mmol/l phosphate buffer; 100%D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 5.4 1 atm300 K
25.4 1 atm290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
FELIX98Molecular Simulations, Inc.data analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 592 NOE-derived distance constraints, 16 dihedral angel restraints and 9 fake distance restraints from disulfide bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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