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- PDB-6otb: NMR structure of alpha conotoxin SII -

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Basic information

Entry
Database: PDB / ID: 6otb
TitleNMR structure of alpha conotoxin SII
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: To Be Published
Title: Structural and Pharmacological Characterization of alpha-Conotoxin SII: The sole member of framework II
Authors: Wilhelm, P. / Chin, Y.K.-Y. / Luna-Ramirez, K. / Tae, H.-S. / King, G.F. / Adams, D.J. / Alewood, P.F.
History
DepositionMay 2, 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 1.2Nov 13, 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 S2


Theoretical massNumber of molelcules
Total (without water)1,7971
Polymers1,7971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1580 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 1797.026 Da / Num. of mol.: 1 / Fragment: residues 51-69 / Source method: obtained synthetically / Source: (synth.) Conus striatus (striated cone) / References: UniProt: P28879
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
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: 20 mM sodium phosphate, 2.1 mM Alpha conotoxin SII, 95% H2O/5% D2O
Label: SII / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
2.1 mMAlpha conotoxin SIInatural abundance1
Sample conditionsIonic strength: 20 mM / Label: SII / 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
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CcpNmr AnalysisCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CcpNmr AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
Details: The authors state that they initially calculated and kept 30 structures according to the structures' target function. Then they selected 20 out of the 30 according to the MolProbity score (i. ...Details: The authors state that they initially calculated and kept 30 structures according to the structures' target function. Then they selected 20 out of the 30 according to the MolProbity score (i.e. stereochemical properties).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 20

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