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- PDB-7n0t: NMR structure of EpI[Y(SO)315Y]-OH -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7n0t
TitleNMR structure of EpI[Y(SO)315Y]-OH
ComponentsAlpha-conotoxin EpI
KeywordsTOXIN / cysteine framework CC-C-C / Alpha4/7 pattern
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 episcopatus (invertebrata)
MethodSOLUTION NMR / simulated annealing / na
Model detailsEpI, unsulfated, 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)613982 Australia
The University Grants Committee, Research Grants Council (RGC)616535 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 26, 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-conotoxin EpI


Theoretical massNumber of molelcules
Total (without water)1,7931
Polymers1,7931
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 EpI


Mass: 1792.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Conus episcopatus (invertebrata) / References: UniProt: P56638
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 EpI[Y(SO3)15Y]-OH, 10 uM DSS, 0.5 uM NaOH, 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: CX0001 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLAlpha-conotoxin EpI[Y(SO3)15Y]-OHnatural abundance1
10 uMDSSnatural abundance1
0.5 uMNaOHnatural abundance1
Sample conditionsIonic strength: 15 mM / Label: H2O/D2O, pH6 / 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 / Details: with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis3CCPNchemical shift assignment
Refinement
MethodSoftware ordinalDetails
simulated annealing2torsion angle simulated annealing, 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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