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- PDB-1e75: NMR SOLUTION STRUCTURE OF ALPHA-CONOTOXIN IM1 POINT MUTATION VARI... -

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Basic information

Entry
Database: PDB / ID: 1.0E+75
TitleNMR SOLUTION STRUCTURE OF ALPHA-CONOTOXIN IM1 POINT MUTATION VARIANT R7L
ComponentsALPHA-CONOTOXIN IM1(R7L)
KeywordsPEPTIDE TOXIN / NEUROTOXIN / NEURONAL NICOTINIC ACETYLCHOLINE RECEPTOR ANTAGONIST / ALPHA-CONOTOXIN / NMR SOLUTION STRUCTURE
Function / homologyConotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Alpha-conotoxin ImI
Function and homology information
Biological speciesCONUS IMPERIALIS (invertebrata)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMISATION
AuthorsRogers, J.P. / Luginbuhl, P. / Pemberton, K. / Harty, P. / Wemmer, D.E. / Stevens, R.C.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structure-Activity Relationships in a Peptidic Alpha7 Nicotinic Acetylcholine Receptor Antagonist
Authors: Rogers, J.P. / Luginbuhl, P. / Pemberton, K. / Harty, P. / Wemmer, D.E. / Stevens, R.C.
#1: Journal: Biochemistry / Year: 1999
Title: NMR Solution Structure of Alpha-Conotoxin Imi and Comparison to Other Conotoxins Specific for Neuronal Nicotinic Acetylcholine Receptors
Authors: Rogers, J.P. / Luginbuhl, P. / Shen, G.S. / Mccabe, R.T. / Stevens, R.C. / Wemmer, D.E.
#2: Journal: Mol.Pharmacol. / Year: 1995
Title: Alpha-Conotoxin Imi Exhibits Subtype-Specific Nicotinic Acetylcholine Receptor Blockade: Preferential Inhibition of Homomeric Alpha7 and Alpha9 Receptors
Authors: Johnson, D.S. / Martinez, J. / Elgoyhen, A.B. / Heinemann, S.F. / Mcintosh, J.M.
#3: Journal: J.Biol.Chem. / Year: 1994
Title: A Nicotinic Acetylcholine Receptor Ligand of Unique Specificity, Alpha-Conotoxin Imi
Authors: Mcintosh, J.M. / Yoshikami, D. / Mahe, E. / Nielsen, D.B. / Rivier, J.E. / Gray, W.R. / Olivera, B.M.
History
DepositionAug 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Structure summary / Category: pdbx_nmr_representative
Item: _pdbx_nmr_representative.conformer_id / _pdbx_nmr_representative.selection_criteria
Revision 1.4Jan 15, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag
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
Revision 1.6Oct 23, 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 IM1(R7L)


Theoretical massNumber of molelcules
Total (without water)1,3131
Polymers1,3131
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 / 40LOWEST RESIDUAL TARGET FUNCTION
RepresentativeModel #12closest to the average

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Components

#1: Protein/peptide ALPHA-CONOTOXIN IM1(R7L)


Mass: 1312.566 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically
Details: SYNTHESIZED USING STANDARD FMOC CHEMISTRY. IM1 SEQUENCE FOUND NATURALLY IN CONUS IMPERIALIS VENOM
Source: (synth.) CONUS IMPERIALIS (invertebrata) / References: UniProt: P50983
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121ROESY
131DQF-COSY
NMR detailsText: DATA CONSIST OF 64 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND 30 ANGLE CONSTRAINTS OBTAINED FROM NOE MEASUREMENTS AND COUPLING CONSTANT MEASUREMENTS. THESE INPUT DATA ARE ALSO ...Text: DATA CONSIST OF 64 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND 30 ANGLE CONSTRAINTS OBTAINED FROM NOE MEASUREMENTS AND COUPLING CONSTANT MEASUREMENTS. THESE INPUT DATA ARE ALSO AVAILABLE FROM THE PROTEIN DATA BANK. THREE STEREOSPECIFIC RESONANCE ASSIGNMENTS HAVE BEEN MADE. TORSION ANGLE DYNAMICS CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA (P. GUNTERT, C. MUMENTHALER, K. WUTHRICH, J. MOL. BIOL. (1997) VOL. 273, 283-298). FOR THE RESTRAINED ENERGY MINIMIZATION THE PROGRAM OPAL (P. LUGINBUHL, P. GUNTERT, M. BILLETER, K. WUTHRICH, J. BIOMOL. NMR (1996) VOL. 8, 136-146) WAS USED. DEPOSITED COORDINATES ARE THOSE OF CONFORMERS 1-20 IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. NO VIOLATIONS OF DISTANCE CONSTRAINTS FROM NOES EXCEED 0.10 ANGSTROMS, AND NO VIOLATIONS OF ANGLE CONSTRAINTS EXCEED 2.0 DEGREES. REPRESENTATIVE CONFORMER HAS THE SMALLEST RMSD TO THE MEAN STRUCTURE UPON SUPERPOSITION OF THE BACKBONE ATOMS N, CA, AND C' OF RESIDUES 2-11.

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Sample preparation

Sample conditionspH: 3.7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
DYANAstructure solution
OPALstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMISATION
Software ordinal: 1
Details: FOR THE PRESENT STRUCTURES THE NMR DISTANCE CONSTRAINTS WERE WEIGHTED SUCH THAT A VIOLATION OF AN UPPER DISTANCE LIMIT OF 0.1 ANGSTROM CORRESPONDS TO AN ENERGY OF KT/2. THE CONSTRAINTS ON ...Details: FOR THE PRESENT STRUCTURES THE NMR DISTANCE CONSTRAINTS WERE WEIGHTED SUCH THAT A VIOLATION OF AN UPPER DISTANCE LIMIT OF 0.1 ANGSTROM CORRESPONDS TO AN ENERGY OF KT/2. THE CONSTRAINTS ON DIHEDRAL ANGLES RESULTING FROM MEASUREMENTS OF VICINAL COUPLING CONSTANTS WERE WEIGHTED SUCH THAT A VIOLATION OF 2.5 DEGREES CORRESPONDS TO AN ENERGY OF KT/2.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: LOWEST RESIDUAL TARGET FUNCTION
Conformers calculated total number: 40 / Conformers submitted total number: 20

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