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- PDB-1ne5: Solution Structure of HERG Specific Scorpion Toxin CnErg1 -

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Basic information

Entry
Database: PDB / ID: 1ne5
TitleSolution Structure of HERG Specific Scorpion Toxin CnErg1
Componentsergtoxin
KeywordsTOXIN / alpha-helix / triple-stranded beta-sheet
Function / homology
Function and homology information


potassium channel inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Potassium channel toxin gamma/Ergtoxin / Ergtoxin family / Ergtoxin family signature. / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium channel toxin gamma-KTx 1.1
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
AuthorsTorres, A.M. / Paramjit, B. / Alewood, P. / Kuchel, P.W. / Vandenberg, J.I.
Citation
Journal: FEBS Lett. / Year: 2003
Title: Solution structure of CnErg1 (Ergtoxin), a HERG specific scorpion toxin
Authors: Torres, A.M. / Bansal, P. / Alewood, P.F. / Bursill, J.A. / Kuchel, P.W. / Vandenberg, J.I.
#1: Journal: FASEB J. / Year: 1999
Title: A toxin to nervous, cardiac, and endocrine ERG K+ channels isolated from Centruroides noxius scorpion venom.
Authors: Gurrola, G.B. / Rosati, B. / Rocchetti, M. / Pimienta, G. / Zaza, A. / Arcangeli, A. / Olivotto, M. / Possani, L.D. / Wanke, E.
#2: Journal: FEBS Lett. / Year: 2000
Title: Disulfide bridges of ergtoxin, a member of a new sub-family of peptide blockers of the ether-a-go-go-related K+ channel
Authors: Scaloni, A. / Bottiglieri, C. / Ferrara, L. / Corona, M. / Gurrola, G.B. / Batista, C. / Wanke, E. / Possani, L.D.
History
DepositionDec 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ergtoxin


Theoretical massNumber of molelcules
Total (without water)4,7461
Polymers4,7461
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 / 4000structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide ergtoxin / CnErg1 / ErgTx


Mass: 4746.415 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Centruroides noxius
References: UniProt: Q86QT3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure were determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.7mM CnErg1 / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no salt added / pH: 3.2 / Pressure: ambient / Temperature: 298 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerprocessing
XEASY1.3.13Bartels, C., Xia, T., Billeter, M., Guntert, P., Wuthrich,K.data analysis
INFITSzyperski, I., Guntert, P., Otting, G., Wuthrich, K.data analysis
NOAHMumenthaler, C., Guntert, P., Braun, W., Wuthrich, K.structure solution
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 578 restraints, 535 are NOE-derived distance restraints, 11 dihedral angle restraints, 32 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 20

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