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Yorodumi- PDB-2i1t: Solution structure of Jingzhaotoxin-III, a novel toxin inhibiting... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i1t | ||||||
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Title | Solution structure of Jingzhaotoxin-III, a novel toxin inhibiting both Nav and Kv channels | ||||||
Components | Jingzhaotoxin-3 | ||||||
Keywords | TOXIN / Jingzhaotoxin-III / Kv2.1 channel / Nav channel / cardiac myocytes / solution structure | ||||||
Function / homology | Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / : / toxin activity / extracellular region / Beta/kappa-theraphotoxin-Cg1a Function and homology information | ||||||
Biological species | Chilobrachys jingzhao (spider) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Liao, Z. / Peng, K. / Liang, S. | ||||||
Citation | Journal: To be Published Title: Solution structure of Jingzhaotoxin-III, a novel toxin inhibiting both Nav and Kv channels Authors: Liao, Z. / Peng, K. / Liang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i1t.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i1t.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 2i1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/2i1t ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i1t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3930.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chilobrachys jingzhao (spider) / Secretion: venom / References: UniProt: P62520 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: TOCSY spectra were obtained with a mixing time of 85 ms. NOESY spectra were recorded in D2O with a mixing time of 200 ms and in H2O with mixing times of 100, 200, and 400 ms. All two- ...Text: TOCSY spectra were obtained with a mixing time of 85 ms. NOESY spectra were recorded in D2O with a mixing time of 200 ms and in H2O with mixing times of 100, 200, and 400 ms. All two-dimensional measurements were recorded with 1024-512 frequency data points and were zero-filled to yield 2048-1024 data matrices except for the high resolution DQF-COSY spectrum. The DQF-COSY spectrum was recorded with 2048-1024 data points in the t2 and t1 dimensions, respectively, and zero-filled to 4096 - 2048 points to measure the coupling constants. |
-Sample preparation
Details | Contents: 6mM Jingzhaotoxin-III, 20mM deuterium sodium acetate buffer, 0.002% NaN3, 0.01mM EDTA, 0.2mM Sodium 3-(trimethylsilyl) propionate-2,2,3,3-d4, pH 4.0, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20mM / pH: 4.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 Details: Structural calculations were performed on 395 interproton distance constraints derived from the 2D NOESY spectra, 13 dihedral angle constraints derived from the coupling constant (DQF-COSY) ...Details: Structural calculations were performed on 395 interproton distance constraints derived from the 2D NOESY spectra, 13 dihedral angle constraints derived from the coupling constant (DQF-COSY) and NOE measurements, eight hydrogen-bond restraints derived from the hydrogen-deuterium exchange experiments, and nine disulfide bond restraints, giving a total of 425 restraints. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |