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- PDB-5ipo: Solution Structure of Hge36: Scorpine-like Peptide from Hadrurus ... -

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Basic information

Entry
Database: PDB / ID: 5ipo
TitleSolution Structure of Hge36: Scorpine-like Peptide from Hadrurus Gertschi
ComponentsHge-scorpine
KeywordsTOXIN / scorpine-like peptide / Hadrurus gertschi / antiparasitic activity
Function / homology
Function and homology information


potassium channel regulator activity / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Long chain scorpion toxin family / Potassium channel toxin / BetaSPN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile.
Similarity search - Domain/homology
Biological speciesHadrurus gertschi (scorpion)
MethodSOLUTION NMR
AuthorsFlores-Solis, D. / Rodriguez De La Vega, R. / del Rio-Portilla, F.
Funding support Mexico, 2items
OrganizationGrant numberCountry
CONSEJO NACIONAL DE CIENCIA Y TECNOLOGIA166472 Mexico
DIRECCION GENERAL DE ASUNTOS DEL PERSONAL ACADEMICO-UNAMIN207713 Mexico
CitationJournal: Febs Lett. / Year: 2016
Title: Solution structure and antiparasitic activity of scorpine-like peptides from Hoffmannihadrurus gertschi.
Authors: Flores-Solis, D. / Toledano, Y. / Rodriguez-Lima, O. / Cano-Sanchez, P. / Ramirez-Cordero, B.E. / Landa, A. / Rodriguez de la Vega, R.C. / Del Rio-Portilla, F.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hge-scorpine


Theoretical massNumber of molelcules
Total (without water)5,3101
Polymers5,3101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein/peptide Hge-scorpine / Hg-scorpine-like 1 / Hgscplike1


Mass: 5310.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadrurus gertschi (scorpion) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q0GY40

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
142isotropic12D 1H-15N HSQC
152isotropic12D 1H-13C HSQC
1102isotropic13D CBCA(CO)NH
192isotropic13D HNCO
182isotropic13D HNCA
172isotropic13D HN(CO)CA
162isotropic13D HN(CA)CB
1112isotropic13D 1H-15N NOESY
1122isotropic13D 1H-15N TOCSY
1132isotropic22D 1H-1H TOCSY
1151isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution13.0 mM Hge36, 95% H2O/5% D2OrHge3695% H2O/5% D2O
solution23.0 mM [U-13C; U-15N] Hge36, 95% H2O/5% D2OrlHge3695% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.0 mMHge36natural abundance1
3.0 mMHge36[U-13C; U-15N]2
Sample conditionsIonic strength: 3 mM / Label: cond_1 / pH: 3.0 / Pressure: 585 mmHg / Temperature: 25 C

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AvanceIIIBrukerAvanceIII7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AMBERCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMR ensembleConformers submitted total number: 20

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