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- PDB-1n8m: Solution structure of Pi4, a four disulfide bridged scorpion toxi... -

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Basic information

Entry
Database: PDB / ID: 1n8m
TitleSolution structure of Pi4, a four disulfide bridged scorpion toxin active on potassium channels
ComponentsPotassium channel blocking toxin 4
KeywordsTOXIN / potassium channel blocker / disulfide bridge stabilized alpha beta motif
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 6.4
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGuijarro, J.I. / M'Barek, S. / Olamendi-Portugal, T. / Gomez-Lagunas, F. / Garnier, D. / Rochat, H. / Possani, L.D. / Sabatier, J.M. / Delepierre, M.
Citation
Journal: Protein Sci. / Year: 2003
Title: Solution structure of Pi4, a short four-disulfide-bridged scorpion toxin specific of potassium channels.
Authors: Guijarro, J.I. / M'Barek, S. / Gomez-Lagunas, F. / Garnier, D. / Rochat, H. / Sabatier, J.M. / Possani, L.D. / Delepierre, M.
#1: Journal: Toxicon / Year: 1998
Title: Two similar peptides from the venom of the scorpion Pandinus imperator, one highly effective blocker and the other inactive on K+ channels
Authors: Olamendi-Portugal, T. / Gomez-Lagunas, F. / Gurrola, G.B. / Possani, L.D.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Revision 1.4Nov 6, 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:
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Assembly

Deposited unit
A: Potassium channel blocking toxin 4


Theoretical massNumber of molelcules
Total (without water)4,1961
Polymers4,1961
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel blocking toxin 4 / Pi4


Mass: 4195.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in the venom of Pandinus imperator scorpions, with an amidated C-terminus. It was established by NMR that the structure of the natural toxin extracted from ...Details: This sequence occurs naturally in the venom of Pandinus imperator scorpions, with an amidated C-terminus. It was established by NMR that the structure of the natural toxin extracted from scorpion venom is effectively identical to the structure of the synthetic toxin, which has a carboxylated C-terminus.
References: UniProt: P58498
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121P-COSY
1322D NOESY
NMR detailsText: Disulfide bridges were determined by NMR and by N-terminal sequencing of proteolysis peptides. Distance constraints were derived from initial nOe build up rates using 2D NOESY experiments with ...Text: Disulfide bridges were determined by NMR and by N-terminal sequencing of proteolysis peptides. Distance constraints were derived from initial nOe build up rates using 2D NOESY experiments with mixing times of 70, 100, 150, 200 and 250 ms in H2O and D2O.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM Pi4, 5 mM CD3COONa, pH 4.0, 10% D2O90% H2O/10% D2O
23.2 mM Pi4, 5 mM CD3COONa, pD 4.0, 100% D2O100% D2O
Sample conditionsIonic strength: 5 / pH: 4 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
NMRView5.03Johnsondata analysis
ARIA1.2Nilgesstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on a total of 705 constraints, 679 are meaningful nOe derived constraints (642 unambiguous, 37 ambiguous), 16 are dihedral (phi) angle constraints and 10 are hydrogen ...Details: Structures are based on a total of 705 constraints, 679 are meaningful nOe derived constraints (642 unambiguous, 37 ambiguous), 16 are dihedral (phi) angle constraints and 10 are hydrogen bonds. The four disulfide bridges (CYS 6-27, 12-32, 16-34, 22-37) were included in the topology file used for the calculations.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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