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- PDB-1pe4: SOLUTION STRUCTURE OF TOXIN CN12 FROM CENTRUROIDES NOXIUS ALFA SC... -

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Basic information

Entry
Database: PDB / ID: 1pe4
TitleSOLUTION STRUCTURE OF TOXIN CN12 FROM CENTRUROIDES NOXIUS ALFA SCORPION TOXIN ACTING ON SODIUM CHANNELS. NMR STRUCTURE
ComponentsNeurotoxin Cn11
KeywordsTOXIN / SCORPION TOXIN / CENTRUROIDES NOXIUS / SODIUM CHANNELS ALPHA TOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / : / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCentruroides noxius (Mexican scorpion)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsDel Rio-Portilla, F. / Hernandez-Marin, E. / Pimienta, G. / Coronas, F.V. / Zamudio, F.Z. / Rodrguez de la Vega, R.C. / Wanke, E. / Possani, L.D.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: NMR solution structure of Cn12, a novel peptide from the Mexican scorpion Centruroides noxius with a typical beta-toxin sequence but with alpha-like physiological activity.
Authors: Del Rio-Portilla, F. / Hernandez-Marin, E. / Pimienta, G. / Coronas, F.V. / Zamudio, F.Z. / Rodrguez de la Vega, R.C. / Wanke, E. / Possani, L.D.
History
DepositionMay 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Remark 999SEQUENCE At the time of processing, no reference database sequence for this protein was available.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotoxin Cn11


Theoretical massNumber of molelcules
Total (without water)7,1551
Polymers7,1551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 250NO RESTRAINT VIOLATIONS LESS THAN 0.2 ANGSTROMS AND MIMINUM ENERGY LESS THAN 115.0 KCAL/MOL BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE: 1
RepresentativeModel #1minimized average structure

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Components

#1: Protein Neurotoxin Cn11 / CN12


Mass: 7154.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: TOXIN OBTAINED DIRECTLY FROM VENOM OF CENTRUROIDES NOXIUS. ACTIVITY IS VERY LOW, HOWEVER CN12 HAS SOME REQUIREMENTS FOR BEING A VERY ACTIVE TOXIN.
Source: (natural) Centruroides noxius (Mexican scorpion) / Secretion: VENOM / References: UniProt: P63019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF COSY, 2D TOCSY, AND 2D NOSEY
222DQF-COSY, 2D TOCSY, AND 2D NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H-1H 2D NMR ON THE NATURAL TOXIN EXTRACTED FROM THE SCORPION VENOM

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM in H2O/D2O 90:10%;90% H2O and 10% D2O
20.6 mM in 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1none 3.1 ambient 300 K
2none 3.1 ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGERrefinement
NMRPipe1DELAGLIOprocessing
VNMR6.1cVARIANcollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE JOURNAL REFERENCE
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATIONS LESS THAN 0.2 ANGSTROMS AND MIMINUM ENERGY LESS THAN 115.0 KCAL/MOL BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE: 1
Conformers calculated total number: 250 / Conformers submitted total number: 19

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