1SN4

STRUCTURE OF SCORPION NEUROTOXIN BMK M4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of two alpha-like scorpion toxins: non-proline cis peptide bonds and implications for new binding site selectivity on the sodium channel.

He, X.L.Li, H.M.Zeng, Z.H.Liu, X.Q.Wang, M.Wang, D.C.

(1999) J.Mol.Biol. 292: 125-135

  • DOI: 10.1006/jmbi.1999.3036
  • Primary Citation of Related Structures:  
  • Also Cited By: 1T7B, 1T7E, 1T7A

  • PubMed Abstract: 
  • The crystal structures of two group III alpha-like toxins from the scorpion Buthus martensii Karsch, BmK M1 and BmK M4, were determined at 1.7 A and 1.3 A resolution and refined to R factors of 0.169 and 0.166, respectively. The first high-resolution ...

    The crystal structures of two group III alpha-like toxins from the scorpion Buthus martensii Karsch, BmK M1 and BmK M4, were determined at 1.7 A and 1.3 A resolution and refined to R factors of 0.169 and 0.166, respectively. The first high-resolution structures of the alpha-like scorpion toxin show some striking features compared with structures of the "classical" alpha-toxin. Firstly, a non-proline cis peptide bond between residues 9 and 10 unusually occurs in the five-member reverse turn 8-12. Secondly, the cis peptide 9-10 mediates the spatial relationship between the turn 8-12 and the C-terminal stretch 58-64 through a pair of main-chain hydrogen bonds between residues 10 and 64 to form a unique tertiary arrangement which features the special orientation of the terminal residues 62-64. Finally, in consequence of the peculiar orientation of the C-terminal residues, the functional groups of Arg58, which are crucial for the toxin-receptor interaction, are exposed and accessible in BmK M1 and M4 rather than buried as in the classical alpha-toxins. Sequence alignment and characteristics analysis suggested that the above structural features observed in BmK M1 and M4 occur in all group III alpha-like toxins. Recently, some group III alpha-like toxins were demonstrated to occupy a receptor site different from the classical alpha-toxin. Therefore, the distinct structural features of BmK M1 and M4 presented here may provide the structural basis for the newly recognized toxin-receptor binding site selectivity. Besides, the non-proline cis peptide bonds found in these two structures play a role in the formation of the structural characteristics and in keeping accurate positions of the functionally crucial residues. This manifested a way to achieve high levels of molecular specificity and atomic precision through the strained backbone geometry.


    Related Citations: 
    • Crystal Structure of an Acidic Neurotoxin from Scorpion Buthus Martensii Karsch at 1.85A Resolution
      Li, H.M.,Wang, D.C.,Jin, L.,ZENG, Z.H.,Hu, R.Q.
      (1996) J.Mol.Biol. 261: 415
    • Crystal Structure of Toxin II from the Scorpion Androctonus Australis Hector Refined at 1.3 A Resolution
      Housset, D.,Habersetzer-Rochat, C.,Astier, J.P.,Fontecilla-Camps, J.C.
      (1994) J.Mol.Biol. 238: 88
    • Purification and Sequence Determination of a New Neutral Mammalian Neurotoxin from the Scorpion Buthus Martensii Karsch
      Luo, M.J.,Xiong, Y.M.,Wang, M.,Wang, D.C.,Chi, C.W.
      (1997) Toxicon 35: 723
    • Purification and Partial Characterization of Several New Neurotoxins from East_ Asia Scorpion Crystallographic Studies on an Acidic Toxin from Scorpion Buthus Martensii Karsch
      Hu, R.Q.,Wang, M.,LIU, J.N.,LEI, K.J.
      (1989) Zool.Res.Sinica. 10: 185
    • Structure of Scorpion Toxin Variant-3 at 1.2 A Resolution
      Zhao, B.,Carson, M.,Ealick, S.E.,Bugg, C.E.
      (1992) J.Mol.Biol. 227: 239


    Organizational Affiliation

    Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P.R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NEUROTOXIN BMK M4)
A
64Mesobuthus martensiiMutation(s): 0 
Find proteins for P58328 (Mesobuthus martensii)
Go to UniProtKB:  P58328
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 54.880α = 90.00
b = 54.880β = 90.00
c = 33.760γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
WEISdata reduction
AMoREphasing
WEISdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-17
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description