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- PDB-6ofa: Wasabi Receptor Toxin -

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Basic information

Entry
Database: PDB / ID: 6ofa
TitleWasabi Receptor Toxin
ComponentsWasabi Receptor Toxin
KeywordsTOXIN / Cysteine-stabilized helical hairpin / TRPA1 / Scorpion / Venom
Function / homologytoxin activity / host cell cytoplasm / extracellular region / Wasabi receptor toxin
Function and homology information
Biological speciesUrodacus manicatus (scorpion)
MethodSOLUTION NMR / simulated annealing
AuthorsLin King, J.V. / Kelly, M.J.S. / Julius, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS105038 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37 NS065071 United States
CitationJournal: Cell / Year: 2019
Title: A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain.
Authors: Lin King, J.V. / Emrick, J.J. / Kelly, M.J.S. / Herzig, V. / King, G.F. / Medzihradszky, K.F. / Julius, D.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wasabi Receptor Toxin


Theoretical massNumber of molelcules
Total (without water)3,8621
Polymers3,8621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Wasabi Receptor Toxin


Mass: 3862.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Urodacus manicatus (scorpion) / References: UniProt: C0HLG4*PLUS

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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 COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H COSY
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H NOESY
172isotropic12D 1H-13C HSQC aliphatic
182isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM Wasabi Receptor Toxin, 90% H2O/10% D2Owater90% H2O/10% D2O
solution2300 uM Wasabi Receptor Toxin, 100% D2Odeuterium100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMWasabi Receptor Toxinnatural abundance1
300 uMWasabi Receptor Toxinnatural abundance2
Sample conditionsIonic strength: 0 M / Ionic strength err: 0 / Label: conditions / pH: 4 / PH err: 0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALINGE, O'DONOGHUE AND NILGESrefinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
PSVSBhattacharya and Montelionedata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 50

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