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- PDB-8f2f: NMR solution structure of lambda-MeuKTx-1 -

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Basic information

Entry
Database: PDB / ID: 8f2f
TitleNMR solution structure of lambda-MeuKTx-1
ComponentsNeurotoxin lambda-MeuTx
KeywordsTOXIN / ICK fold / inhibitor cystine knot
Function / homologypotassium channel regulator activity / calcium channel regulator activity / toxin activity / extracellular region / Neurotoxin lambda-MeuTx
Function and homology information
Biological speciesMesobuthus eupeus (lesser Asian scorpion)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Craik, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biosci Rep / Year: 2013
Title: Functional evolution of scorpion venom peptides with an inhibitor cystine knot fold.
Authors: Gao, B. / Harvey, P.J. / Craik, D.J. / Ronjat, M. / De Waard, M. / Zhu, S.
History
DepositionNov 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotoxin lambda-MeuTx


Theoretical massNumber of molelcules
Total (without water)4,1361
Polymers4,1361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area2910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neurotoxin lambda-MeuTx / Calcium channel toxin-like peptide-1


Mass: 4135.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mesobuthus eupeus (lesser Asian scorpion) / References: UniProt: P86399
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-13C HSQC aliphatic
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H NOESY
172isotropic12D ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM peptide, 90% H2O/10% D2Osample 190% H2O/10% D2O
solution21.0 mM peptide, 100% D2Osample 2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMpeptidenatural abundance1
1.0 mMpeptidenatural abundance2
Sample conditionsIonic strength: nd Not defined / Label: conditions_1 / pH: 3.0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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