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- PDB-1ttk: NMR solution structure of omega-conotoxin MVIIA, a N-type calcium... -

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Basic information

Entry
Database: PDB / ID: 1ttk
TitleNMR solution structure of omega-conotoxin MVIIA, a N-type calcium channel blocker
ComponentsOmega-conotoxin MVIIa
KeywordsTOXIN / four loop frame work / amidated C-terminal / disulfide rich
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Conotoxin / Conotoxin
Similarity search - Domain/homology
Omega-conotoxin MVIIA
Similarity search - Component
MethodSOLUTION NMR / Solution structures were calculated using torsion angle dynamics, simulated annealing techniques.
AuthorsAdams, D.J. / Smith, A.B. / Schroeder, C.I. / Yasuda, T. / Lewis, R.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: omega-conotoxin CVID inhibits a pharmacologically distinct voltage-sensitive calcium channel associated with transmitter release from preganglionic nerve terminals
Authors: Adams, D.J. / Smith, A.B. / Schroeder, C.I. / Yasuda, T. / Lewis, R.J.
#1: Journal: to be published
Title: The alfa2delta auxiliary subunit reduces the affinity of omega-conotoxins for recombinant N-type calcium channels
Authors: Mould, J. / Yasuda, T. / Schroeder, C.I. / Beedle, A.M. / Doering, C.J. / Zamponi, G.W. / Adams, D.J. / Lewis, R.J.
History
DepositionJun 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Omega-conotoxin MVIIa


Theoretical massNumber of molelcules
Total (without water)2,6501
Polymers2,6501
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 / 50structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: Protein/peptide Omega-conotoxin MVIIa


Mass: 2650.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Conus magus / References: UniProt: P05484
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
1422D NOESY
1522D TOCSY
162E-COSY
NMR detailsText: This structure was detrmined using standard 2D homonucelar NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM MVIIA, 95% H2O, D2O, DSS95% H2O/5% D2O
22mM MVIIA, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.5ambient 293 K
23.5ambient 280 K

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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
Bruker DRXBrukerDRX5001
Bruker AMXBrukerAMX7502

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
X-PLOR3.851structure solution
X-PLOR3.851refinement
RefinementMethod: Solution structures were calculated using torsion angle dynamics, simulated annealing techniques.
Software ordinal: 1
Details: A total of 456 distance restraints (including H-bonds) and 31 dihedral distance restraints (including 22 phis and 9 chi angles) were used to calculate the structure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 17

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