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- PDB-7m1e: Structural and functional studies about scorpine showed the prese... -

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Basic information

Entry
Database: PDB / ID: 7m1e
TitleStructural and functional studies about scorpine showed the presence of blocking channel and cytolytic activities as well as two different structural domains
ComponentsScorpine
KeywordsTOXIN / scorpion toxins / potassium channels / scorpine like-peptides / cytolytic peptides
Function / homologyLong chain scorpion toxin family / Potassium channel toxin / BetaSPN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / other organism cell membrane / toxin activity / defense response to bacterium / extracellular region / membrane / Scorpine
Function and homology information
Biological speciesPandinus imperator (emperor scorpion)
MethodSOLUTION NMR / molecular dynamics
Authorsdel Rio, J.F. / Lopez, A.E. / Titaux, G.
CitationJournal: Toxicon / Year: 2022
Title: Structural and functional studies of scorpine: A channel blocker and cytolytic peptide.
Authors: Lopez-Giraldo, E. / Carrillo, E. / Titaux-Delgado, G. / Cano-Sanchez, P. / Colorado, A. / Possani, L.D. / Rio-Portilla, F.D.
History
DepositionMar 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scorpine


Theoretical massNumber of molelcules
Total (without water)3,1361
Polymers3,1361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Scorpine / Scorpin / Panscorpine


Mass: 3135.679 Da / Num. of mol.: 1 / Fragment: N-terminal residues 20-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pandinus imperator (emperor scorpion) / Production host: Escherichia coli (E. coli) / References: UniProt: P56972

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 5 mM N-terminal extreme scorpine, trifluoroethanol/water
Label: 1H / Solvent system: trifluoroethanol/water
SampleConc.: 5 mM / Component: N-terminal extreme scorpine / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.5Keller and Wuthrichchemical shift assignment
CARA1.5Keller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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