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- PDB-6cuc: Solution structure of double knot toxin (DkTx) -

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Basic information

Entry
Database: PDB / ID: 6cuc
TitleSolution structure of double knot toxin (DkTx)
ComponentsTau-theraphotoxin-Hs1a
KeywordsTOXIN / ICK / spider toxin / dktx / trpv1 / tarantula
Function / homologyion channel regulator activity / toxin activity / lipid binding / extracellular region / Tau-theraphotoxin-Hs1a
Function and homology information
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
AuthorsRamanujam, V. / Mobli, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structural Basis of the Bivalency of the TRPV1 Agonist DkTx.
Authors: Ramanujam, V. / Crawford, T. / Cristofori-Armstrong, B. / Deuis, J.R. / Jia, X. / Maxwell, M.J. / Jami, S. / Ma, L. / Vetter, I. / Mobli, M.
History
DepositionMar 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
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_spectrometer.model / _struct_conn.pdbx_dist_value
Revision 1.2Apr 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tau-theraphotoxin-Hs1a


Theoretical massNumber of molelcules
Total (without water)9,2881
Polymers9,2881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1medoid

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Components

#1: Protein Tau-theraphotoxin-Hs1a / Tau-TRTX-Hs1a / Double-knot toxin / DkTx


Mass: 9287.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma schmidti (Chinese earth tiger)
Production host: Escherichia coli (E. coli) / References: UniProt: P0CH43

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] DkTx, 20 mM sodium phosphate, 10 uM DSS, 0.02 % w/v sodium azide, 95% H2O/5% D2O
Label: 13C/15N sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDkTx[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
10 uMDSSnatural abundance1
0.02 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 5.8 / PH err: 0.05 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CcpNMRCCPNdata analysis
RNMRTKHoch and Sternprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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