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- PDB-2mpq: Solution structure of the sodium channel toxin Hd1a -

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Basic information

Entry
Database: PDB / ID: 2mpq
TitleSolution structure of the sodium channel toxin Hd1a
ComponentsHd1a
KeywordsTOXIN / Spider toxin / Disulfide-rich peptide / Sodium channel / Knottin / Inhibitor cystine knot
Function / homologyHuwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / : / toxin activity / extracellular region / Mu-theraphotoxin-Hd1a
Function and homology information
Biological speciesHaplopelma doriae (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsBest MobProbity score, model 1
AuthorsKlint, J.K. / Mobli, M. / King, G.F.
CitationJournal: Br.J.Pharmacol. / Year: 2015
Title: Seven novel modulators of the analgesic target NaV 1.7 uncovered using a high-throughput venom-based discovery approach.
Authors: Klint, J.K. / Smith, J.J. / Vetter, I. / Rupasinghe, D.B. / Er, S.Y. / Senff, S. / Herzig, V. / Mobli, M. / Lewis, R.J. / Bosmans, F. / King, G.F.
History
DepositionJun 1, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 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: Hd1a


Theoretical massNumber of molelcules
Total (without water)3,8911
Polymers3,8911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200Best MobProbity score
RepresentativeModel #1best mobprobity score

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Components

#1: Protein/peptide Hd1a


Mass: 3891.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma doriae (spider) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J9X1W9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D 1H-15N NOESY
1813D HBHA(CO)NH
1914D HCC(CO)NH
NMR detailsText: NOESY MIXING TIME 200ms

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Sample preparation

DetailsContents: 20 mM sodium acetate, 0.5 mM [U-98% 13C; U-98% 15N] Hd1a, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetate-11
0.5 mMHd1a-2[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 20 / pH: 4.9 / 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
NameVersionDeveloperClassification
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3.1Bruker Biospincollection
Rowland_NMR_Toolkit3Stern, Mobli, Hochprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 702 / NOE intraresidue total count: 178 / NOE long range total count: 214 / NOE medium range total count: 142 / NOE sequential total count: 168 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 28 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: best mobprobity score
NMR ensembleConformer selection criteria: Best MobProbity score / Conformers calculated total number: 200 / Conformers submitted total number: 20

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