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- PDB-6btv: Solution NMR structures for CcoTx-II -

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Basic information

Entry
Database: PDB / ID: 6btv
TitleSolution NMR structures for CcoTx-II
ComponentsBeta-theraphotoxin-Cm1b
KeywordsTOXIN / spider / disulfide / ICK / pain / NaV1.7 / voltage gated ion channel
Function / homologyHuwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin / sodium channel inhibitor activity / : / toxin activity / extracellular space / Beta-theraphotoxin-Cm1b
Function and homology information
Biological speciesCeratogyrus marshalli (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsAgwa, A.J. / Schroeder, C.I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1080405 Australia
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Gating modifier toxins isolated from spider venom: Modulation of voltage-gated sodium channels and the role of lipid membranes.
Authors: Agwa, A.J. / Peigneur, S. / Chow, C.Y. / Lawrence, N. / Craik, D.J. / Tytgat, J. / King, G.F. / Henriques, S.T. / Schroeder, C.I.
History
DepositionDec 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Beta-theraphotoxin-Cm1b


Theoretical massNumber of molelcules
Total (without water)4,1061
Polymers4,1061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area2830 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Beta-theraphotoxin-Cm1b / Beta-TRTX-Cm1b / Ceratotoxin-2 / CcoTx2


Mass: 4105.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ceratogyrus marshalli (spider) / References: UniProt: P84508

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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 TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-13C HSQC
152isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1 mg/mL CcoTx-II, 90% H2O/10% D2OCcoTx-II90% H2O/10% D2O
solution20.1 mg/mL CcoTx-II, 100% D2OCCoTx-II D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mg/mLCcoTx-IInatural abundance1
0.1 mg/mLCcoTx-IInatural abundance2
Sample conditionsIonic strength units: Not defined / Label: CcoTx-II / pH: 6 / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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