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- PDB-2kni: High-resolution solution structure of the ASIC1a blocker PcTX1 -

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Basic information

Entry
Database: PDB / ID: 2kni
TitleHigh-resolution solution structure of the ASIC1a blocker PcTX1
ComponentsPsalmotoxin-1
KeywordsTOXIN / Psalmotoxin 1 / pi-theraphotoxin-Pc1a / cystine knot / spider toxin / peptide toxin / Disulfide bond / Ionic channel inhibitor / Knottin / Neurotoxin / Secreted / ASIC1a inhibitor / acid sensing ion channel 1a inhibitor
Function / homologyLaminin - #10 / Laminin / ion channel regulator activity / Other non-globular / Special / toxin activity / extracellular region / Psalmotoxin-1
Function and homology information
Biological speciesPsalmopoeus cambridgei (Trinidad chevron tarantula)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsBest MolProbity score, model 1
AuthorsKing, G.F. / Mobli, M. / Saez, N.J.
Citation
Journal: Mol.Pharmacol. / Year: 2011
Title: A dynamic pharmacophore drives the interaction between Psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a.
Authors: Saez, N.J. / Mobli, M. / Bieri, M. / Chassagnon, I.R. / Malde, A.K. / Gamsjaeger, R. / Mark, A.E. / Gooley, P.R. / Rash, L.D. / King, G.F.
#1: Journal: Protein Sci. / Year: 2003
Title: Recombinant production and solution structure of PcTx1, the specific peptide inhibitor of ASIC1a proton-gated cation channels.
Authors: Escoubas, P. / Bernard, C. / Lambeau, G. / Lazdunski, M. / Darbon, H.
History
DepositionAug 25, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Psalmotoxin-1


Theoretical massNumber of molelcules
Total (without water)4,7931
Polymers4,7931
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)25 / 300Best MolProbity score
RepresentativeModel #1best molprobity score

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Components

#1: Protein/peptide Psalmotoxin-1 / PcTx1


Mass: 4792.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psalmopoeus cambridgei (Trinidad chevron tarantula)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P60514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D C(CO)NH
1613D H(CCO)NH
1712D 1H-15N HSQC
1813D HNHB
1914D HC(CO)NH-TOCSY
11023D 1H-13C NOESY
NMR detailsText: This structure was determined using a combination of NOESY-derived distance restraints, TALOS-derived dihedral-angle restraints, and hydrogen-bond restraints derived from a long-range HNCO ...Text: This structure was determined using a combination of NOESY-derived distance restraints, TALOS-derived dihedral-angle restraints, and hydrogen-bond restraints derived from a long-range HNCO experiment. The author shows the MolProbity statistics as follows. MOLPROBITY OUTPUT SCORES: AVERAGE ALL-ATOM CLASHSCORE 0.0, AVERAGE RAMACHANDRAN OUTLIERS 0.0%, AVERAGE RAMACHANDRAN FAVORED 83.9%, AVERAGE MOLPROBITY SCORE 1.68, AVERAGE MOLPROBITY PERCENTILE RANK 89.4

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-99% 13C; U-99% 15N] PcTx1-1, 93% H2O/7% D2O93% H2O/7% D2O
20.3 mM [U-99% 13C; U-99% 15N] PcTx1-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPcTx1-1[U-99% 13C; U-99% 15N]1
0.3 mMPcTx1-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 10 / pH: 6.0 / 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
CYANA2.1P.GUNTERT ET AL.refinement
CYANA2.1P.GUNTERT ET AL.structure solution
XEASYBartels et al.chemical shift assignment
Rowland_NMR_ToolkitHoch, Stern et al.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: best molprobity score
NMR ensembleConformer selection criteria: Best MolProbity score / Conformers calculated total number: 300 / Conformers submitted total number: 25 / Representative conformer: 1

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