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- PDB-1lup: Solution structure of a toxin (GsMTx2) from the tarantula, Grammo... -

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Basic information

Entry
Database: PDB / ID: 1lup
TitleSolution structure of a toxin (GsMTx2) from the tarantula, Grammostola spatulata, which inhibits mechanosensitive ion channels
ComponentsGsMTx2
KeywordsTOXIN / inhibitor cysteine knot / beta-sheet
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Kappa-theraphotoxin-Gr2a
Function and homology information
Biological speciesGrammostola rosea (Chilean rose tarantula)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsOswald, R.E. / Suchyna, T.M. / McFeeters, R. / Gottlieb, P. / Sachs, F.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Solution structure of peptide toxins that block mechanosensitive ion channels
Authors: Oswald, R.E. / Suchyna, T.M. / McFeeters, R. / Gottlieb, P. / Sachs, F.
#1: Journal: J.GEN.PHYSIOL. / Year: 2000
Title: Identification of a peptide toxin from Grammostola spatulata spider venom that blocks stretch-activated channels.
Authors: Suchyna, T.M. / Johnson, J.H. / Hamer, K. / Leykam, J.F. / Gage, D.A. / Clemo, H.F. / Baumgarten, C.M. / Sachs, F.
History
DepositionMay 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 30, 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:
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Assembly

Deposited unit
A: GsMTx2


Theoretical massNumber of molelcules
Total (without water)3,9351
Polymers3,9351
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 / 200structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide GsMTx2


Mass: 3934.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Grammostola rosea (Chilean rose tarantula)
Secretion: venom / References: UniProt: P60273*PLUS
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
2212D NOESY
3312D NOESY
4412D NOESY
5512D NOESY
461DQF-COSY
5712D-TOCSY
4811H 15N-HSQC
1922D NOESY
21022D NOESY
31122D NOESY
41222D NOESY
4132E-COSY
41421H 13C-HSQC
NMR detailsText: H-D exchange using 2D TOCSY following resuspension of lyophilized protein in 100% D2O

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM natural abundance GsMTx210% D2O, pH 4.5
22 mM natural abundance GsMTx2100% D2O, pH 4.5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11 mM NaCl 4.5ambient 278 K
21 mM NaCl 4.5ambient 289 K
31 mM NaCl 4.5ambient 293 K
41 mM NaCl 4.5ambient 298 K
51 mM NaCl 4.5ambient 308 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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2.2Accelrys, Inc.processing
NMRPipe2.1Delaglioprocessing
Sparky3.95Goddarddata analysis
CNS1.1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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