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Yorodumi- PDB-5t3m: Solution structure of a triple mutant of HwTx-IV - a potent block... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t3m | ||||||
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Title | Solution structure of a triple mutant of HwTx-IV - a potent blocker of Nav1.7 | ||||||
Components | Mu-theraphotoxin-Hs2a | ||||||
Keywords | TOXIN | ||||||
Function / homology | Function and homology information host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Haplopelma schmidti (Chinese earth tiger) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Rahnama, S. / Sharma, G. / Mobli, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: PLoS ONE / Year: 2017 Title: The structure, dynamics and selectivity profile of a NaV1.7 potency-optimised huwentoxin-IV variant. Authors: Rahnama, S. / Deuis, J.R. / Cardoso, F.C. / Ramanujam, V. / Lewis, R.J. / Rash, L.D. / King, G.F. / Vetter, I. / Mobli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t3m.cif.gz | 247.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t3m.ent.gz | 209.2 KB | Display | PDB format |
PDBx/mmJSON format | 5t3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/5t3m ftp://data.pdbj.org/pub/pdb/validation_reports/t3/5t3m | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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Details | Monomer as determined by NMR and mass spectrometry |
-Components
#1: Protein/peptide | Mass: 3999.777 Da / Num. of mol.: 1 / Fragment: residues 53-87 / Mutation: E1G,E4G,Y33W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haplopelma schmidti (Chinese earth tiger) Plasmid: PLIC-C Details (production host): MBP fusion - periplasmic export sequence Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P83303 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 400 uM [U-99% 13C; U-99% 15N] [m3]-HwTx-IV, 20 mM sodium acetate, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O Details: 300 ul sample, added into a susceptibility matched 5 mm NMR cells (Shigemi Inc. Japan), prepared by dissolving 15N/13C-labled m3-HwTx-IV to a final concentration of 400 uM in 20 mM sodium acetate solution, pH 5. Label: 15N/13C [m3]-HwTx-IV / Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 mM / Ionic strength err: 1 / Label: peptide sample / pH: 5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0 / Temperature: 298 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 2 / Details: automated NOE assignments | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |