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- PDB-2n6o: Structure of spider-venom peptide Hm1a -

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Basic information

Entry
Database: PDB / ID: 2n6o
TitleStructure of spider-venom peptide Hm1a
ComponentsKappa-theraphotoxin-Hm1a
KeywordsTOXIN / Hm1a / spider venom / cystine knot / gating modifier
Function / homologyregulation of voltage-gated sodium channel activity / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / : / sodium channel regulator activity / toxin activity / extracellular region / Delta-theraphotoxin-Hm1a
Function and homology information
Biological speciesHeteroscodra maculata (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsUndheim, E.A.B. / King, G.F. / Mobli, M.
Citation
Journal: To be Published
Title: Structure of spider-venom peptide Hm1a
Authors: Undheim, E.A.B. / King, G.F. / Mobli, M. / Petrou, S.
#1: Journal: Mol.Pharmacol. / Year: 2002
Title: Novel tarantula toxins for subtypes of voltage-dependent potassium channels in the Kv2 and Kv4 subfamilies.
Authors: Escoubas, P. / Diochot, S. / Celerier, M.L. / Nakajima, T. / Lazdunski, M.
History
DepositionAug 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-theraphotoxin-Hm1a


Theoretical massNumber of molelcules
Total (without water)4,0081
Polymers4,0081
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 / 300MolProbity score
RepresentativeModel #1molprobity score

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Components

#1: Protein/peptide Kappa-theraphotoxin-Hm1a / Kappa-TRTX-Hm1a / Heteroscodratoxin-1 / HmTx1


Mass: 4008.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Heteroscodra maculata (spider) / References: UniProt: P60992

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.0 mM Hm1a, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.0 mM / Component: Hm1a-1
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNMRCCPNdata analysis
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angle estimation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: molprobity score
NMR ensembleConformer selection criteria: MolProbity score / Conformers calculated total number: 300 / Conformers submitted total number: 20

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