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- PDB-1jlp: Solution Structure of the Noncompetitive Skeletal Muscle Nicotini... -

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Basic information

Entry
Database: PDB / ID: 1jlp
TitleSolution Structure of the Noncompetitive Skeletal Muscle Nicotinic Acetylcholine Receptor Antagonist Psi-conotoxin PIIIF
ComponentsPSI-CONOTOXIN PIIIF
KeywordsTOXIN / MULTIPLE DISULFIDE BONDS / AMIDATED C-TERMINUS
Function / homologyhost cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Psi-conotoxin PIIIF
Function and homology information
MethodSOLUTION NMR / distance geometry molecular dynamics relaxation matrix distance geometry simulated annealing
AuthorsVan Wagoner, R.M. / Ireland, C.M.
Citation
Journal: Biochemistry / Year: 2003
Title: Characterization and Three-Dimensional Structure Determination of psi-Conotoxin Piiif, a Novel Noncompetitive Antagonist of Nicotinic Acetylcholine Receptors
Authors: Van Wagoner, R.M. / Ireland, C.M.
#1: Journal: Biochemistry / Year: 1998
Title: Three-dimensional Solution Structure of Conotoxin psi-PIIIE, an Acetylcholine Gated Ion Channel Antagonist
Authors: Mitchell, S.S. / Shon, K.J. / Foster, M.P. / Davis, D.R. / Olivera, B.M. / Ireland, C.M.
#2: Journal: Biochemistry / Year: 1997
Title: A Noncompetitive Peptide Inhibitor of the Nicotinic Acetylcholine Receptor from Conus purpurascens Venom
Authors: Shon, K.J. / Grilley, M. / Jacobsen, R. / Cartier, G.E. / Hopkins, C. / Gray, W.R. / Watkins, M. / Hillyard, D.R. / Rivier, J. / Torres, J. / Yoshikami, D. / Olivera, B.M.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSI-CONOTOXIN PIIIF


Theoretical massNumber of molelcules
Total (without water)2,6741
Polymers2,6741
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)17 / 50back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #12closest to the average

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Components

#1: Protein/peptide PSI-CONOTOXIN PIIIF


Mass: 2674.157 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid phase chemical synthesis was used. One sample contained only natural isotopic abundance residues. Another peptide incorporated 3-13C-labeled cysteine at position 4. The third peptide ...Details: Solid phase chemical synthesis was used. One sample contained only natural isotopic abundance residues. Another peptide incorporated 3-13C-labeled cysteine at position 4. The third peptide incorporated 3-13C-labeled cysteine at positions 5, 10, 16, 21, and 22. The sequence for all peptides is the same as the native peptide FROM CONUS PURPURASCENS (PURPLE CONE).
References: UniProt: P60245

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
232PE-COSY
14313C-selected 2D NOESY
15413C-selected 2D NOESY
164Double half-filtered 2D NOESY
274Double half-filtered 2D PE-COSY
28413C-selected 1D 1H NMR
NMR detailsText: This structure was determined using isotopic filtration and isotope-selected 1H observation in addition to standard homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
112 mM psi-conotoxin PIIIF; TFA added to pH 3.590% H2O/10% D2O
212 mM psi-conotoxin PIIIF100% D2O
314 mM of psi-conotoxin PIIIF [5,10,16,21,22] 3-13C-Cys; TFA added to pH 3.590% H2O/10% D2O
416 mM of psi-conotoxin PIIIF [4] 3-13C-Cys; TFA added to pH 3.590% H2O/10% D2O
516 mM of psi-conotoxin PIIIF [4] 3-13C-Cys100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
112 mM; tetra-TFA salt 3.5ambient 277 K
212 mM; tetra-TFA salt 3.5ambient 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian, Inc.collection
Felix97MSI, Inc.processing
IRMA97MSI, Inc.iterative matrix relaxation
DGII97MSI, Inc.structure solution
Discover2.98MSI, Inc.structure solution
Discover2.98MSI, Inc.refinement
RefinementMethod: distance geometry molecular dynamics relaxation matrix distance geometry simulated annealing
Software ordinal: 1
Details: These structures are based on 380 NOE-derived distance restraints, 7 restraints on phi derived from J-coupling, and 7 restraints on chi1 determined from J-coupling and NOE volumes.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 17

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