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- PDB-7knn: Solution structure of the alpha-conotoxin analogue [2-8]-alkyne Vc1.1 -

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Basic information

Entry
Database: PDB / ID: 7knn
TitleSolution structure of the alpha-conotoxin analogue [2-8]-alkyne Vc1.1
ComponentsAlpha-conotoxin Vc1a
KeywordsTOXIN / Conotoxin dicarba
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
Alpha-conotoxin Vc1a
Similarity search - Component
Biological speciesConus victoriae (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMacRaild, C.A. / Robinson, S.D. / Chhabra, S. / Norton, R.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP120100414 Australia
CitationJournal: J.Med.Chem. / Year: 2021
Title: Alkyne-Bridged alpha-Conotoxin Vc1.1 Potently Reverses Mechanical Allodynia in Neuropathic Pain Models.
Authors: Belgi, A. / Burnley, J.V. / MacRaild, C.A. / Chhabra, S. / Elnahriry, K.A. / Robinson, S.D. / Gooding, S.G. / Tae, H.S. / Bartels, P. / Sadeghi, M. / Zhao, F.Y. / Wei, H. / Spanswick, D. / ...Authors: Belgi, A. / Burnley, J.V. / MacRaild, C.A. / Chhabra, S. / Elnahriry, K.A. / Robinson, S.D. / Gooding, S.G. / Tae, H.S. / Bartels, P. / Sadeghi, M. / Zhao, F.Y. / Wei, H. / Spanswick, D. / Adams, D.J. / Norton, R.S. / Robinson, A.J.
History
DepositionNov 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin Vc1a


Theoretical massNumber of molelcules
Total (without water)1,7781
Polymers1,7781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Alpha-conotoxin Vc1a / Alpha-Vc1a / ACV1 / Vc1.1


Mass: 1777.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus victoriae (invertebrata) / References: UniProt: P69747
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-15N soFastHMQC
252isotropic12D 1H-1H NOESY
262isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mg/mL [2-8]-alkyne Vc1.1, 90% H2O/10% D2O190% H2O/10% D2O
solution21 mg/mL [2-8]-alkyne Vc1.1, 100% D2O1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mL[2-8]-alkyne Vc1.1natural abundance1
1 mg/mL[2-8]-alkyne Vc1.1natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 M14.8 1 atm298 K
20 M14.8 pH*1 atm298 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
NameVersionDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIH2.4Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.4Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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