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- PDB-2mt7: Solution structure of spider-venom peptide Hs1a -

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Basic information

Entry
Database: PDB / ID: 2mt7
TitleSolution structure of spider-venom peptide Hs1a
ComponentsHs1a
KeywordsTOXIN / spider-venom peptide / inhibitor cystine knot / Nav1.7 / Nav channel inhibitor / ION CHANNEL MODULATOR
Function / homologyHuwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / toxin activity / extracellular region / Hs1a
Function and homology information
Biological speciesHysterocrates (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsMolProbity score, model1
AuthorsKlint, J.K. / King, G.F. / Mobli, M.
CitationJournal: To be Published
Title: Nav1.7 inhibitors normalise mechanical responses in chronic visceral hypersensitivity
Authors: Klint, J.K. / Castro, J. / Vetter, I. / Er, S.Y. / Cardoso, F. / Liu, Y. / Hagan, R. / Neff, R. / Minassian, N. / Huang, J.X. / Cooper, M.A. / Wickenden, A. / Mobli, M. / Jin, L. / ...Authors: Klint, J.K. / Castro, J. / Vetter, I. / Er, S.Y. / Cardoso, F. / Liu, Y. / Hagan, R. / Neff, R. / Minassian, N. / Huang, J.X. / Cooper, M.A. / Wickenden, A. / Mobli, M. / Jin, L. / Nicolazzo, J.A. / Lewis, R.J. / Bosmans, F. / Brierley, S.M. / King, G.F.
History
DepositionAug 14, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: 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 1.2Oct 9, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hs1a


Theoretical massNumber of molelcules
Total (without water)3,8671
Polymers3,8671
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 / 200MolProbity score
RepresentativeModel #1molprobity score

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Components

#1: Protein/peptide Hs1a


Mass: 3866.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hysterocrates (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KKS8*PLUS
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of spider-venom peptide Hs1a
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1814D HCC(CO)NH TOCSY
NMR detailsText: All 3D/4D data other than NOESY data acquired with NUS and processed using maximum entropy reconstruction

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Sample preparation

DetailsContents: 0.5 mM [U-98% 13C; U-98% 15N] Hs1a-1, 20 mM sodium acetate-2, 5 % D2O-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHs1a-1[U-98% 13C; U-98% 15N]1
20 mMsodium acetate-21
5 %D2O-31
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
TopSpin3.1Bruker Biospincollection
Rowland_NMR_Toolkit3Jeffrey C. Hoch & Alan Sternprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
TALOS+Cornilescu, Delaglio and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Using automated NOE assignments
NMR constraintsNOE constraints total: 702 / NOE intraresidue total count: 182 / NOE long range total count: 223 / NOE medium range total count: 103 / NOE sequential total count: 194 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 26
NMR representativeSelection criteria: molprobity score
NMR ensembleConformer selection criteria: MolProbity score / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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