2OSH

crystal structure of Natratoxin, a snake sPLA2 that blocks A-type K+ channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents.

Hu, P.Sun, L.Zhu, Z.Q.Hou, X.W.Wang, S.Yu, S.S.Wang, H.L.Zhang, P.Wang, M.Niu, L.W.Teng, M.K.Ruan, D.Y.

(2008) Proteins 72: 673-683

  • DOI: 10.1002/prot.21964

  • PubMed Abstract: 
  • Snake secreted phospholipasesA2 (sPLA2s) are widely used as pharmacological tools to investigate their role in diverse pathophysiological processes. Some members of snake venom sPLA2s have been found to block voltage-activated K(+) channels (K(v) cha ...

    Snake secreted phospholipasesA2 (sPLA2s) are widely used as pharmacological tools to investigate their role in diverse pathophysiological processes. Some members of snake venom sPLA2s have been found to block voltage-activated K(+) channels (K(v) channels). However, most studies involved in their effects on ion channels were indirectly performed on motor nerve terminals while few studies were directly done on native neurons. Here, a novel snake sPLA2 peptide neurotoxin, Natratoxin, composed of 119 amino acid residues and purified from Naja atra venom was reported. It was characterized using whole-cell patch-clamp in acutely dissociated rat dorsal root ganglion (DRG) neurons. It was found to effectively inhibit A-type K(+) currents and cause alterations of channel gating characters, such as the shifts of steady-state activation and inactivation curves to hyperpolarization direction and changes of V(1/2) and slope factor. Therefore, Natratoxin was suggested to be a gating modifier of K(v) channel. In addition, this inhibitory effect was found to be independent of its enzymatic activity. These results suggested that the toxin enacted its inhibitory effect by binding to K(v) channel. To further elucidate the structural basis for this electrophysiological phenomenon, we determined the crystal structure of Natratoxin at 2.2 A resolution by molecular replacement method and refined to an R-factor of 0.190. The observed overall fold has a different structural organization from other K(+) channel inhibitors in animal toxins. Compared with other K(v) channel inhibitors, a similar putative functional surface in its C-terminal was revealed to contribute to protein-protein interaction in such a blocking effect. Our results demonstrated that the spatial distribution of key amino acid residues matters most in the recognition of this toxin towards its channel target rather than its type of fold.


    Organizational Affiliation

    Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, HeFei, Anhui, 230027, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2 1
A
119Naja atraMutation(s): 0 
EC: 3.1.1.4
Find proteins for A4FS04 (Naja atra)
Go to UniProtKB:  A4FS04
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 42.078α = 90.00
b = 42.078β = 90.00
c = 64.117γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MAR345data collection
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-02-06 
  • Released Date: 2007-03-03 
  • Deposition Author(s): Teng, M.K., Sun, L.

Revision History 

  • Version 1.0: 2007-03-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description