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- PDB-2lr9: High-resolution solution NMR structure of the rho-conotoxin TIA. -

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Basic information

Entry
Database: PDB / ID: 2lr9
TitleHigh-resolution solution NMR structure of the rho-conotoxin TIA.
ComponentsRho-conotoxin TIA
KeywordsTOXIN / rho-conotoxin
Function / homologyConotoxin, alpha-type / Alpha conotoxin precursor / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / toxin activity / extracellular region / Rho-conotoxin TIA
Function and homology information
Biological speciesConus tulipa (tulip cone)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRosengren, K. / Lewis, R.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Conopeptide rho-TIA defines a new allosteric site on the extracellular surface of the alpha 1B-adrenoceptor.
Authors: Ragnarsson, L. / Wang, C.I. / Andersson, A. / Fajarningsih, D. / Monks, T. / Brust, A. / Rosengren, K.J. / Lewis, R.J.
History
DepositionMar 27, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 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: Rho-conotoxin TIA


Theoretical massNumber of molelcules
Total (without water)2,4001
Polymers2,4001
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 acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Rho-conotoxin TIA / Rho-TIA


Mass: 2399.953 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide was made synthetically through solid phase peptide chemistry.
Source: (synth.) Conus tulipa (tulip cone) / References: UniProt: P58811
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Refined solution NMR structure of the rho-conotoxin TIA.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mg/mL conotoxin TIA-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mg/mL / Component: conotoxin TIA-1
Sample conditionsIonic strength: 0 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Initial structures were calculated using torsion angle dynamics within CNS. The structures were subsequently refined and energy minimized using restrained Cartesian molecular dynamics in explicit water.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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