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- PDB-5tlr: Solution NMR structure of gHwTx-IV -

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Basic information

Entry
Database: PDB / ID: 5tlr
TitleSolution NMR structure of gHwTx-IV
ComponentsMu-theraphotoxin-Hs2a
KeywordsTOXIN / spider toxin / disulfide-rich / sodium channel inhibitor
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAgwa, A.J. / Schroeder, C.I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1080405 Australia
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7.
Authors: Agwa, A.J. / Lawrence, N. / Deplazes, E. / Cheneval, O. / Chen, R.M. / Craik, D.J. / Schroeder, C.I. / Henriques, S.T.
History
DepositionOct 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 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 1.4Jun 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-Hs2a


Theoretical massNumber of molelcules
Total (without water)4,0371
Polymers4,0371
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 / 50all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Mu-theraphotoxin-Hs2a / Mu-TRTX-Hs2a / Huwentoxin-4 / Huwentoxin-IV / HwTx-IV / Huwentoxin-IVa / HWTX-IVa / Huwentoxin-IVb ...Mu-TRTX-Hs2a / Huwentoxin-4 / Huwentoxin-IV / HwTx-IV / Huwentoxin-IVa / HWTX-IVa / Huwentoxin-IVb / HWTX-IVb / Huwentoxin-IVc / HWTX-IVc


Mass: 4036.820 Da / Num. of mol.: 1 / Fragment: UNP residues 54-87 / Mutation: E56G, Y58W, F85W / Source method: obtained synthetically / Source: (synth.) Haplopelma schmidti (Chinese earth tiger) / References: UniProt: P83303

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D 1H
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC
1122isotropic12D E.COSY
2112isotropic12D 1H-1H TOCSY
2102isotropic12D 1H-1H NOESY
292isotropic11D 1H
381isotropic22D 1H-1H TOCSY
371isotropic21D 1H

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution190 % H2O, 10 % D2O, 90% H2O/10% D2OgHwTx-IV_H2O90% H2O/10% D2O
solution2100 % D2O, 100% D2OgHwTx-IV_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
90 %H2Onone1
10 %D2Onone1
100 %D2Onone2
Sample conditions
Conditions-IDIonic strength unitsLabelpHPressure (kPa)Temperature (K)Details
1Not definedgHwTx-IV_H2O4.0 ambient 298 K
2Not definedgHwTx-IV_D2O4.0 ambient 298 K
3Not definedgHwTx-IV_Tempvar4.0 ambient 283 KTemperature variation experiment with temperatures ranging from 283 - 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Cryoprobe
Bruker AVANCEBrukerAVANCE5002

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Processing

SoftwareName: CNS / Classification: refinement
NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOS-NCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MolProbityRichardsondata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 5
Details: the structures are based on a total of 437 restraints, 385 are NOE-derived distance constraints, 10 distance restraints from hydrogen bonds, 42 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 20

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