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 2NDI | pdb_00002ndi

Solution structure of the toxin ISTX-I from Ixodes scapularis


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2NDI

This is version 1.2 of the entry. See complete history. 

Literature

A sodium channel inhibitor ISTX-I with a novel structure provides a new hint at the evolutionary link between two toxin folds.

Rong, M., Liu, J., Zhang, M., Wang, G., Zhao, G., Wang, G., Zhang, Y., Hu, K., Lai, R.

(2016) Sci Rep 6: 29691-29691

  • DOI: https://doi.org/10.1038/srep29691
  • Primary Citation Related Structures: 
    2NDI

  • PubMed Abstract: 

    Members of arachnida, such as spiders and scorpions, commonly produce venom with specialized venom glands, paralyzing their prey with neurotoxins that specifically target ion channels. Two well-studied motifs, the disulfide-directed hairpin (DDH) and the inhibitor cystine knot motif (ICK), are both found in scorpion and spider toxins. As arachnids, ticks inject a neurotoxin-containing cocktail from their salivary glands into the host to acquire a blood meal, but peptide toxins acting on ion channels have not been observed in ticks. Here, a new neurotoxin (ISTX-I) that acts on sodium channels was identified from the hard tick Ixodes scapularis and characterized. ISTX-I exhibits a potent inhibitory function with an IC50 of 1.6 μM for sodium channel Nav1.7 but not other sodium channel subtypes. ISTX-I adopts a novel structural fold and is distinct from the canonical ICK motif. Analysis of the ISTX-I, DDH and ICK motifs reveals that the new ISTX-I motif might be an intermediate scaffold between DDH and ICK, and ISTX-I is a clue to the evolutionary link between the DDH and ICK motifs. These results provide a glimpse into the convergent evolution of neurotoxins from predatory and blood-sucking arthropods.


  • Organizational Affiliation: 
    • Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences &Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China.

Macromolecule Content 

  • Total Structure Weight: 4.79 kDa 
  • Atom Count: 328 
  • Modeled Residue Count: 46 
  • Deposited Residue Count: 46 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative secreted salivary protein46Ixodes scapularisMutation(s): 0 
UniProt
Find proteins for Q4PN35 (Ixodes scapularis)
Explore Q4PN35 
Go to UniProtKB:  Q4PN35
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4PN35
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2017-06-07 
  • Deposition Author(s): Hu, K.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary