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- PDB-2naj: Solution structure of K2 lobe of double-knot toxin -

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Basic information

Entry
Database: PDB / ID: 2naj
TitleSolution structure of K2 lobe of double-knot toxin
ComponentsTau-theraphotoxin-Hs1a
KeywordsTOXIN / trpv1 / toxins / tarantula / spider / ICK / double-knot toxin / DkTx / K2
Function / homologyion channel regulator activity / toxin activity / lipid binding / extracellular region / Tau-theraphotoxin-Hs1a
Function and homology information
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBae, C. / Anselmi, C. / Kalia, J. / Jara-Oseguera, A. / Schwieters, C.D. / Krepkiy, D. / Lee, C.W. / Kim, E.H. / Kim, J.I. / Faraldo-Gomez, J.D. / Swartz, K.J.
CitationJournal: Elife / Year: 2016
Title: Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin
Authors: Bae, C. / Anselmi, C. / Kalia, J. / Jara-Oseguera, A. / Schwieters, C.D. / Krepkiy, D. / Lee, C.W. / Kim, E.H. / Kim, J.I. / Faraldo-Gomez, J.D. / Swartz, K.J.
History
DepositionJan 4, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.2Nov 6, 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: Tau-theraphotoxin-Hs1a


Theoretical massNumber of molelcules
Total (without water)3,6861
Polymers3,6861
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Tau-theraphotoxin-Hs1a / Tau-TRTX-Hs1a / Double-knot toxin / DkTx


Mass: 3686.290 Da / Num. of mol.: 1 / Fragment: K2 domain, UNP residues 43-75 / Source method: obtained synthetically / Source: (synth.) Haplopelma schmidti (Chinese earth tiger) / References: UniProt: P0CH43
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
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 mM K2-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: K2-1
Sample conditionspH: 4 / 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
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 476 / NOE intraresidue total count: 180 / NOE long range total count: 118 / NOE medium range total count: 21 / NOE sequential total count: 129 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 6 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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