+Open data
-Basic information
Entry | Database: PDB / ID: 2mi5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of insect-specific sodium channel toxin mu-Dc1a | ||||||
Components | Mu-diguetoxin-Dc1a | ||||||
Keywords | TOXIN / spider venom / insecticidal toxin / sodium channel / voltage-sensor / gating modifier / non-uniform sampling / DTX9.2 / inhibitor cystine knot / knottin | ||||||
Function / homology | Function and homology information host cell presynaptic membrane / sodium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Diguetia canities (spider) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | Best MolProbity score, model1 | ||||||
Authors | Bende, N.S. / Mobli, M. / King, G.F. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: A distinct sodium channel voltage-sensor locus determines insect selectivity of the spider toxin Dc1a. Authors: Bende, N.S. / Dziemborowicz, S. / Mobli, M. / Herzig, V. / Gilchrist, J. / Wagner, J. / Nicholson, G.M. / King, G.F. / Bosmans, F. #1: Journal: Insect Biochem.Mol.Biol. / Year: 1995 Title: Characterization and cloning of insecticidal peptides from the primitive weaving spider Diguetia canities. Authors: Krapcho, K.J. / Kral, R.M. / Vanwagenen, B.C. / Eppler, K.G. / Morgan, T.K. #2: Journal: Toxicon / Year: 1996 Title: Mode of action of an insecticidal peptide toxin from the venom of a weaving spider (Diguetia canities). Authors: Bloomquist, J.R. / Kinne, L.P. / Deutsch, V. / Simpson, S.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mi5.cif.gz | 385.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mi5.ent.gz | 331.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/2mi5 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/2mi5 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 6502.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Diguetia canities (spider) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49126 |
---|---|
Sequence details | VESTIGE OF PROTEASE RECOGNITIO |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: All 3D and 4D except NOESY type data were acquired using non-uniform sampling and processed using maximum entropy. |
-Sample preparation
Details | Contents: 350 uM [U-99% 13C; U-99% 15N] Dc1a-1, 20 mM sodium acetate-2, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | Ionic strength: 0.02 / pH: 5.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 902 / NOE intraresidue total count: 267 / NOE long range total count: 276 / NOE medium range total count: 106 / NOE sequential total count: 253 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: best molprobity score | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Best MolProbity score / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |