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- PDB-2i1t: Solution structure of Jingzhaotoxin-III, a novel toxin inhibiting... -

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Basic information

Entry
Database: PDB / ID: 2i1t
TitleSolution structure of Jingzhaotoxin-III, a novel toxin inhibiting both Nav and Kv channels
ComponentsJingzhaotoxin-3
KeywordsTOXIN / Jingzhaotoxin-III / Kv2.1 channel / Nav channel / cardiac myocytes / solution structure
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region / Beta/kappa-theraphotoxin-Cg1a
Function and homology information
Biological speciesChilobrachys jingzhao (spider)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLiao, Z. / Peng, K. / Liang, S.
Citation
Journal: To be Published
Title: Solution structure of Jingzhaotoxin-III, a novel toxin inhibiting both Nav and Kv channels
Authors: Liao, Z. / Peng, K. / Liang, S.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Jingzhaotoxin-III, a novel spider toxin inhibiting activation of voltage-gated sodium channel in rat cardiac myocytes
Authors: Xiao, Y. / Tang, J. / Yang, Y. / Wang, M. / Hu, W. / Xie, J. / Zeng, X. / Liang, S.
History
DepositionAug 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: 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: 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 1.4Oct 16, 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: Jingzhaotoxin-3


Theoretical massNumber of molelcules
Total (without water)3,9311
Polymers3,9311
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 Jingzhaotoxin-3 / Jingzhaotoxin-III / JZTX-III


Mass: 3930.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chilobrachys jingzhao (spider) / Secretion: venom / References: UniProt: P62520
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: TOCSY spectra were obtained with a mixing time of 85 ms. NOESY spectra were recorded in D2O with a mixing time of 200 ms and in H2O with mixing times of 100, 200, and 400 ms. All two- ...Text: TOCSY spectra were obtained with a mixing time of 85 ms. NOESY spectra were recorded in D2O with a mixing time of 200 ms and in H2O with mixing times of 100, 200, and 400 ms. All two-dimensional measurements were recorded with 1024-512 frequency data points and were zero-filled to yield 2048-1024 data matrices except for the high resolution DQF-COSY spectrum. The DQF-COSY spectrum was recorded with 2048-1024 data points in the t2 and t1 dimensions, respectively, and zero-filled to 4096 - 2048 points to measure the coupling constants.

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Sample preparation

DetailsContents: 6mM Jingzhaotoxin-III, 20mM deuterium sodium acetate buffer, 0.002% NaN3, 0.01mM EDTA, 0.2mM Sodium 3-(trimethylsilyl) propionate-2,2,3,3-d4, pH 4.0, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM / pH: 4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH 2.9.6Brunger A. T. etallrefinement
Felix98Biosym Technologiesdata analysis
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Structural calculations were performed on 395 interproton distance constraints derived from the 2D NOESY spectra, 13 dihedral angle constraints derived from the coupling constant (DQF-COSY) ...Details: Structural calculations were performed on 395 interproton distance constraints derived from the 2D NOESY spectra, 13 dihedral angle constraints derived from the coupling constant (DQF-COSY) and NOE measurements, eight hydrogen-bond restraints derived from the hydrogen-deuterium exchange experiments, and nine disulfide bond restraints, giving a total of 425 restraints.
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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