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- PDB-5ug3: NMR SOLUTION STRUCTURE OF ALPHA-CONOTOXIN GID MUTANT A10V -

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Basic information

Entry
Database: PDB / ID: 5ug3
TitleNMR SOLUTION STRUCTURE OF ALPHA-CONOTOXIN GID MUTANT A10V
ComponentsAlpha-conotoxin GID
KeywordsTOXIN / Neurotoxin / neuronal nicotinic acetylcholine receptors
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 geographus (geography cone)
MethodSOLUTION NMR / simulated annealing
AuthorsHussein, A.K. / Leffler, A.E. / Zebroski, H.A. / Powell, S.R. / Kuryatov, A. / Filipenko, P. / Gorson, J. / Heizmann, A. / Lyskov, S. / Nicke, A. ...Hussein, A.K. / Leffler, A.E. / Zebroski, H.A. / Powell, S.R. / Kuryatov, A. / Filipenko, P. / Gorson, J. / Heizmann, A. / Lyskov, S. / Nicke, A. / Lindstrom, J. / Rudy, B. / Bonneau, R. / Holford, M. / Poget, S.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1253277 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models.
Authors: Leffler, A.E. / Kuryatov, A. / Zebroski, H.A. / Powell, S.R. / Filipenko, P. / Hussein, A.K. / Gorson, J. / Heizmann, A. / Lyskov, S. / Tsien, R.W. / Poget, S.F. / Nicke, A. / Lindstrom, J. ...Authors: Leffler, A.E. / Kuryatov, A. / Zebroski, H.A. / Powell, S.R. / Filipenko, P. / Hussein, A.K. / Gorson, J. / Heizmann, A. / Lyskov, S. / Tsien, R.W. / Poget, S.F. / Nicke, A. / Lindstrom, J. / Rudy, B. / Bonneau, R. / Holford, M.
History
DepositionJan 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 4, 2019Group: Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions / Item: _pdbx_nmr_exptl_sample_conditions.temperature
Revision 1.5Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin GID


Theoretical massNumber of molelcules
Total (without water)2,1771
Polymers2,1771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Alpha-conotoxin GID


Mass: 2177.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus geographus (geography cone) / References: UniProt: P60274

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic22D 1H-1H TOCSY
124isotropic22D 1H-1H NOESY
134isotropic22D DQF-COSY
143isotropic12D 1H-13C HSQC
153isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution31.5 mM A10V design 5 mutant, 100% D2OD20 conditions100% D2O
solution41.5 mM A10V design 5 mutant, 90% H2O/10% D2OH20 conditions90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMA10V design 5 mutantnone3
1.5 mMA10V design 5 mutantnone4
Sample conditionsIonic strength: 0 Not defined / Label: Condition1 / pH: 3 / PH err: 0.05 / Pressure: 1 atm / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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