1SN1

STRUCTURE OF SCORPION NEUROTOXIN BMK M1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 

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:  
    1SN1, 1SN4

  • 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 structures of the alpha-like scorpion toxin show some striking features compared with structures of the "classical" alpha-toxin ...

    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 1.85 A Resolution
      Li, H.M., Wang, D.C., Zeng, Z.H., Jin, L., Hu, R.Q.
      (1996) J Mol Biol 261: 415
    • Two Neurotoxins (Bmk I and Bmk II) from the Venom of the Scorpion Buthus Martensii Karsch-Purification, Amino Acid Sequence and Assessment of Specific Activity
      Ji, Y.H., Mansuelle, P., Terakawa, S., Kopeyan, C.
      (1996) Toxicon 34: 987
    • 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
    • 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
    • Purification and Partial Characterization of Several New Neurotoxins from East- Asia Scorpion [Chinese]
      Hu, R.Q., Wang, M., Liu, J.N., Lei, K.J.
      (1989) Dongwuxue Yanjiu 10: 185
    • Structure of Variant-3 Scorpion Neurotoxin from Centruroides Sculpturatus Ewing, Refined at 1.8 A Resolution
      Almassy, R.J., Fontecilla-Camps, J.C., Suddath, F.L., Bugg, C.E.
      (1983) J Mol Biol 170: 496
    • Three-Dimensional Structure of a Protein from Scorpion Venom. A New Structural Class of Neurotoxins
      Fontecilla-Camps, J.C., Almassy, R.J., Suddath, F.L., Watt, D.D., Bugg, C.E.
      (1980) Proc Natl Acad Sci U S A 77: 6496

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NEUROTOXIN BMK M1)A64Mesobuthus martensiiMutation(s): 0 
UniProt
Find proteins for P45697 (Mesobuthus martensii)
Explore P45697 
Go to UniProtKB:  P45697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45697
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.42α = 90
b = 41.09β = 90
c = 23.93γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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