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- PDB-5t4r: NMR solution structure of the Nav1.7 selective spider venom-deriv... -

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Basic information

Entry
Database: PDB / ID: 5t4r
TitleNMR solution structure of the Nav1.7 selective spider venom-derived peptide Pn3a
ComponentsMu-theraphotoxin-Pn3a
KeywordsTOXIN / tarantula peptide toxin / inhibitor cystine knot / voltage-gated sodium channel modifier / voltage sensor modifier
Biological speciesTheraphosidae (tarantulas)
MethodSOLUTION NMR / simulated annealing
AuthorsRosengren, K.J. / Armstrong, D.A. / Vetter, I.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Sci Rep / Year: 2017
Title: Pharmacological characterisation of the highly Na V 1.7 selective spider venom peptide Pn3a.
Authors: Deuis, J.R. / Dekan, Z. / Wingerd, J.S. / Smith, J.J. / Munasinghe, N.R. / Bhola, R.F. / Imlach, W.L. / Herzig, V. / Armstrong, D.A. / Rosengren, K.J. / Bosmans, F. / Waxman, S.G. / Dib- ...Authors: Deuis, J.R. / Dekan, Z. / Wingerd, J.S. / Smith, J.J. / Munasinghe, N.R. / Bhola, R.F. / Imlach, W.L. / Herzig, V. / Armstrong, D.A. / Rosengren, K.J. / Bosmans, F. / Waxman, S.G. / Dib-Hajj, S.D. / Escoubas, P. / Minett, M.S. / Christie, M.J. / King, G.F. / Alewood, P.F. / Lewis, R.J. / Wood, J.N. / Vetter, I.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name
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: Mu-theraphotoxin-Pn3a


Theoretical massNumber of molelcules
Total (without water)4,2861
Polymers4,2861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2860 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50lowest energy and covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mu-theraphotoxin-Pn3a


Mass: 4285.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Theraphosidae (tarantulas)

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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-15N HSQC
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-13C HSQC
172isotropic12D 1H-1H ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mg/mL mu-theraphotoxin-Pn3a, 90% H2O/10% D2OH2O sample90% H2O/10% D2O
solution22 mg/mL mu-theraphotoxin-Pn3a, 100% D2OD2O sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLmu-theraphotoxin-Pn3anatural abundance1
2 mg/mLmu-theraphotoxin-Pn3anatural abundance2
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / pH: 4 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: equipped with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin2.1Bruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy and covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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