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- PDB-1tyk: SOLUTION STRUCTURE OF A TOXIN FROM THE TARANTULA, GRAMMOSTOLA SPA... -

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Basic information

Entry
Database: PDB / ID: 1tyk
TitleSOLUTION STRUCTURE OF A TOXIN FROM THE TARANTULA, GRAMMOSTOLA SPATULATA, WHICH INHIBITS MECHANOSENSITIVE ION CHANNELS
ComponentsToxin GsMTx-4
KeywordsTOXIN / INHIBITOR / CYSTEINE KNOT / BETA-SHEET
Function / homology
Function and homology information


ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / defense response to bacterium / lipid binding / extracellular region
Similarity search - Function
Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
M-theraphotoxin-Gr1a
Similarity search - Component
Biological speciesGrammostola rosea (Chilean rose tarantula)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RAMACHANDRAN REFINEMENT
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 Cation-Selective 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.
#2: Journal: Toxicon / Year: 2003
Title: cDNA sequence and in vitro folding of GsMTX4, a specific peptide inhibitor of mechanosensitive channels
Authors: Ostrow, K.L. / Mammoser, A. / Suchyna, T. / Sachs, F. / Oswald, R. / Kubo, S. / Chino, N. / Gottlieb, P.A.
History
DepositionJul 8, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJul 13, 2004ID: 1LQR
Revision 1.0Jul 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 13, 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: Toxin GsMTx-4


Theoretical massNumber of molelcules
Total (without water)4,1101
Polymers4,1101
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 Toxin GsMTx-4 / MTx4


Mass: 4109.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VENOM
Source: (natural) Grammostola rosea (Chilean rose tarantula)
References: UniProt: Q7YT39
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
121DQF-COSY
131E-COSY
1412D TOCSY
1511H-13C-HSQC
1611H-15N-HSQC
NMR detailsText: H-D EXCHANGE USING 2D TOCSY FOLLOWING RESUSPENSION OF LYOPHILIZED PROTEIN IN 100% D2O

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Sample preparation

DetailsContents: 2 MM NATURAL ABUNDANCE GSMTX4 / Solvent system: H2O
Sample conditionsIonic strength: 1 mM NACL / pH: 4.5 / Pressure: AMBIENT / Temperature: 278 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felix2.2structure solution
NMRPipe2.1Delagliostructure solution
Sparky3.95Goddardstructure solution
CNS2.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RAMACHANDRAN REFINEMENT
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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