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- PDB-7n1z: NMR structure of native PnIA -

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Basic information

Entry
Database: PDB / ID: 7n1z
TitleNMR structure of native PnIA
ComponentsAlpha-conotoxin PnIA
KeywordsTOXIN / alpha-conotoxin / CC-C-C framework / alpha4/7 pattern / sulfotyrosine
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 PnIA
Function and homology information
Biological speciesConus pennaceus (invertebrata)
MethodSOLUTION NMR / simulated annealing / na
Model detailsPnIA, tyrosine sulfated, C-terminal amide
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 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 20, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin PnIA


Theoretical massNumber of molelcules
Total (without water)1,7061
Polymers1,7061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area1360 Å2
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 PnIA / Alpha-PnIA


Mass: 1705.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Conus pennaceus (invertebrata) / References: UniProt: P50984
Has ligand of interestY
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 PnIA, 10 uM [U-99% 2H] DSS, 90% H2O/10% D2O
Details: 90% H2O, 10% D2O, 10 uM 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS), pH 6.0
Label: NR0004 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLAlpha-conotoxin PnIAnatural abundance1
10 uMDSS[U-99% 2H]1
Sample conditionsDetails: 90% H2O, 10% D2O, 10 uM 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS), pH 6.0
Ionic strength: 5 mM / Label: aqueous / pH: 6 / 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
CARAKeller and Wuthrichchemical shift assignment
Refinement
MethodSoftware ordinalDetails
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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