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- PDB-6v6t: Solution structure of delta-theraphotoxin-Hm1b from Heteroscodra ... -

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Basic information

Entry
Database: PDB / ID: 6v6t
TitleSolution structure of delta-theraphotoxin-Hm1b from Heteroscodra maculata
ComponentsDelta-theraphotoxin-Hm1b
KeywordsTOXIN / spider toxin / inhibitor / cystine knot
Function / homologymodulation of voltage-gated sodium channel activity in another organism / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / : / sodium channel regulator activity / toxin activity / extracellular region / Delta-theraphotoxin-Hm1b
Function and homology information
Biological speciesHeteroscodra maculata (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.Y. / Chow, C.Y. / King, G.F.
CitationJournal: Biochem Pharmacol / Year: 2020
Title: A selective Na V 1.1 activator with potential for treatment of Dravet syndrome epilepsy.
Authors: Chow, C.Y. / Chin, Y.K.Y. / Ma, L. / Undheim, E.A.B. / Herzig, V. / King, G.F.
History
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_volume
Revision 1.3Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-theraphotoxin-Hm1b


Theoretical massNumber of molelcules
Total (without water)3,9941
Polymers3,9941
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 / 30structures with the lowest energy and with best stereochemical properties
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Delta-theraphotoxin-Hm1b / Delta-TRTX-Hm1b


Mass: 3993.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heteroscodra maculata (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DOC5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic12D 1H-1H NOESY
131isotropic22D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 325 uM [U-99% 15N] Hm1b, 20 mM sodium phosphate, 95% H2O/5% D2O
Label: 15N-Hm1b / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
325 uMHm1b[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and with best stereochemical properties
Conformers calculated total number: 30 / Conformers submitted total number: 20

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