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- PDB-2n8f: Chemical shift assignments and structure calculation of spider to... -

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Basic information

Entry
Database: PDB / ID: 2n8f
TitleChemical shift assignments and structure calculation of spider toxin pi-hexatoxin-Hi1a
Componentsspider toxin pi-hexatoxin-Hi1a
KeywordsTOXIN / Spider toxin / Inhibitor cystine knot / double knot toxin / ASIC1a antagonist / Ion channel modulator
Function / homologytoxin activity / extracellular region / Pi-hexatoxin-Hi1a
Function and homology information
Biological speciesHadronyche infensa (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Pineda, S.S. / Mobli, M. / King, G.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Potent neuroprotection after stroke afforded by a double-knot spider-venom peptide that inhibits acid-sensing ion channel 1a.
Authors: Chassagnon, I.R. / McCarthy, C.A. / Chin, Y.K. / Pineda, S.S. / Keramidas, A. / Mobli, M. / Pham, V. / De Silva, T.M. / Lynch, J.W. / Widdop, R.E. / Rash, L.D. / King, G.F.
History
DepositionOct 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: spider toxin pi-hexatoxin-Hi1a


Theoretical massNumber of molelcules
Total (without water)8,7501
Polymers8,7501
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 / 30structures with best stereochemical properties
RepresentativeModel #1best stereochemical properties

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Components

#1: Protein spider toxin pi-hexatoxin-Hi1a


Mass: 8750.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadronyche infensa (spider) / Plasmid: pLICC vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A1L1QJU3*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 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D 1H-15N NOESY

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] hi1a, 10 uM DSS, 0.02 % sodium azide, 20 mM MES, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMhi1a-1[U-99% 13C; U-99% 15N]1
10 uMDSS-21
0.02 %sodium azide-31
20 mMMES-41
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
Rowland_NMR_ToolkitHoch JCprocessing nus data
Rowland_NMR_ToolkitHoch JCprocessing
CYANA3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: best stereochemical properties
NMR ensembleConformer selection criteria: structures with best stereochemical properties
Conformers calculated total number: 30 / Conformers submitted total number: 20

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