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- PDB-2mxo: NMR structure of spider toxin- G7W/N24S mutant of TRTX-Hhn2b -

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Basic information

Entry
Database: PDB / ID: 2mxo
TitleNMR structure of spider toxin- G7W/N24S mutant of TRTX-Hhn2b
ComponentsMu-theraphotoxin-Hhn2b
KeywordsTOXIN / Spider toxin / Voltage gated ion channel / NaV1.7
Function / homologyHuwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region / Mu-theraphotoxin-Hhn2b 3
Function and homology information
Biological speciesHaplopelma hainanum (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsKlint, J.K. / Chin, Y.K.Y. / Mobli, M.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Rational Engineering Defines a Molecular Switch That Is Essential for Activity of Spider-Venom Peptides against the Analgesics Target NaV1.7
Authors: Klint, J.K. / Chin, Y.K. / Mobli, M.
History
DepositionJan 8, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu-theraphotoxin-Hhn2b


Theoretical massNumber of molelcules
Total (without water)3,7931
Polymers3,7931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30Stereochemical property by Molprobity
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mu-theraphotoxin-Hhn2b / GWHhn2b / Mu-TRTX-Hhn2b / Hainantoxin-1.3 / Hainantoxin-I.3 / HnTx-I.3 / Peptide F5-19.03


Mass: 3793.464 Da / Num. of mol.: 1 / Fragment: UNP residues 49-81 / Mutation: G7W, N24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma hainanum (spider) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D2Y1X8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HBHA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1813D 1H-15N NOESY
1913D (H)CCH-TOCSY
11013D HBHA(CO)NH

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] GWHhn2b-1, 20 mM Sodium acetate-2, 5 % D2O-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMGWHhn2b-1[U-99% 13C; U-99% 15N]1
20 mMSodium acetate-21
5 %D2O-31
Sample conditionsIonic strength: 20 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
CcpNmr Analysis2.4CCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Stereochemical property by Molprobity
Conformers calculated total number: 30 / Conformers submitted total number: 20 / Representative conformer: 1

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