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- PDB-7n23: NMR structure of AnIB[Y(SO3)16Y]-OH -

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Basic information

Entry
Database: PDB / ID: 7n23
TitleNMR structure of AnIB[Y(SO3)16Y]-OH
ComponentsAlpha-conotoxin AnIB
KeywordsTOXIN / alpha-conotoxin / CC-C-C framework / alpha4/7 pattern / unsulfated
Function / homologyConotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Alpha-conotoxin AnIB
Function and homology information
Biological speciesConus anemone (invertebrata)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / na
Model detailsAnIB, tyrosine not sulfated, C-terminal acid
AuthorsConibear, A.C. / Rosengren, K.J. / Lee, H.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)616535 Australia
The University Grants Committee, Research Grants Council (RGC)613982 Australia
CitationJournal: Rsc Med Chem / Year: 2021
Title: Posttranslational modifications of alpha-conotoxins: sulfotyrosine and C-terminal amidation stabilise structures and increase acetylcholine receptor binding.
Authors: Ho, T.N.T. / Lee, H.S. / Swaminathan, S. / Goodwin, L. / Rai, N. / Ushay, B. / Lewis, R.J. / Rosengren, K.J. / Conibear, A.C.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 23, 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: Alpha-conotoxin AnIB


Theoretical massNumber of molelcules
Total (without water)1,7151
Polymers1,7151
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Alpha-conotoxin AnIB


Mass: 1714.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Conus anemone (invertebrata) / References: UniProt: P0C1V7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H-1H TOCSY
121isotropic11H-1H NOESY
131isotropic11H-15N HSQC
141isotropic11H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.0 mg/mL Alpha-conotoxin AnIB[Y(SO3)16Y]-OH, 10 uM DSS, 90% H2O/10% D2O
Details: 90% H2O, 10% D2O, 10 uM 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS), pH 3.0
Label: CX0014 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLAlpha-conotoxin AnIB[Y(SO3)16Y]-OHnatural abundance1
10 uMDSSnatural abundance1
Sample conditionsDetails: 90% H2O, 10% D2O, 10 uM 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS), pH 3.0
Ionic strength: 5 mM / Label: aqueous / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARAv3Keller and Wuthrichchemical shift assignment
Refinement
MethodSoftware ordinalDetails
DGSA-distance geometry simulated annealing2torsion angle simulated annealing, ensemble contains 20 structures with the best MolProbity scores, minimum energies and no violations
na1minimised in a water shell
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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