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- PDB-6ovj: NMR structure of truncated alpha conotoxin SII: Ile-SII(3-14) -

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Basic information

Entry
Database: PDB / ID: 6ovj
TitleNMR structure of truncated alpha conotoxin SII: Ile-SII(3-14)
ComponentsAlpha-conotoxin S2
KeywordsTOXIN
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature.
Similarity search - Domain/homology
Biological speciesConus striatus (striated cone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Wilhelm, P. / Alewood, P.F.
CitationJournal: Acs Chem Neurosci / Year: 2022
Title: Cysteine-Rich alpha-Conotoxin SII Displays Novel Interactions at the Muscle Nicotinic Acetylcholine Receptor.
Authors: Wilhelm, P. / Luna-Ramirez, K. / Chin, Y.K. / Dekan, Z. / Abraham, N. / Tae, H.S. / Chow, C.Y. / Eagles, D.A. / King, G.F. / Lewis, R.J. / Adams, D.J. / Alewood, P.F.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2Oct 11, 2023Group: 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_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: Alpha-conotoxin S2


Theoretical massNumber of molelcules
Total (without water)1,3151
Polymers1,3151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Alpha-conotoxin S2 / Alpha-conotoxin SII


Mass: 1314.535 Da / Num. of mol.: 1 / Fragment: residues 52-64 / Source method: obtained synthetically / Source: (synth.) Conus striatus (striated cone) / References: UniProt: P28879

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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
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1.7 mM Ile3-14 SII, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O
Label: Ile-SII(3-14) / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMIle3-14 SIInatural abundance1
20 mMsodium phosphatenatural abundance1
5 %D2Onatural abundance1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 30 / Conformers submitted total number: 20

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