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- PDB-2h8s: Solution structure of alpha-conotoxin Vc1.1 -

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Basic information

Entry
Database: PDB / ID: 2h8s
TitleSolution structure of alpha-conotoxin Vc1.1
ComponentsAlpha-conotoxin Vc1A
KeywordsTOXIN / alpha-conotoxin / alpha-helix / disulfide bonds / amidated C-terminus
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
MethodSOLUTION NMR / torsion angle dynamics
AuthorsClark, R.J. / Fischer, H. / Nevin, S.T. / Adams, D.J. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Synthesis, Structural Characterization, and Receptor Specificity of the {alpha}-Conotoxin Vc1.1.
Authors: Clark, R.J. / Fischer, H. / Nevin, S.T. / Adams, D.J. / Craik, D.J.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)1,8121
Polymers1,8121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 Vc1A / alpha-conotoxin Vc1.1 / Alpha-Vc1A / ACV1


Mass: 1812.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / References: UniProt: P69747
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141E-COSY

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Sample preparation

DetailsContents: approximately 1mM Vc1.1, 90% H2O, 10% D2O, pH 3.5 / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
XwinNMR2.5Brukerprocessing
Sparky3.11Goddard and Knellerdata analysis
DYANA1.5Guntertstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
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: 50 / Conformers submitted total number: 20

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