1CHZ

A NEW NEUROTOXIN FROM BUTHUS MARTENSII KARSCH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A.

He, X.L.Deng, J.P.Wang, M.Zhang, Y.Wang, D.C.

(2000) Acta Crystallogr D Biol Crystallogr 56: 25-33

  • DOI: https://doi.org/10.1107/s0907444999014614
  • Primary Citation of Related Structures:  
    1CHZ

  • PubMed Abstract: 

    A new neurotoxin BmK M2, toxic to both mammals and insects, with the strongest toxicity in the BmK toxin series, has been purified from the Chinese scorpion Buthus martensii Karsch and crystallized with MPD at pH 7.5. The crystals are orthorhombic, belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 36.64, b = 36.95, c = 37.23 A. The structure was solved by molecular replacement and refined to R = 0.186 for all reflections to a resolution of 1.76 A. The whole sequence (64 residues) of BmK M2 was determined by crystallographic analysis based on high-resolution data and the homologous model of BmK M8. The refined BmK M2 structure shows a non-proline cis peptide bond between Pro9 and His10 which enables the C-terminal segment to adopt a conformation different to that of the weak toxin BmK M8. Recently, a mutation analysis had suggested that both the tenth residue and the C-terminus play key roles in receptor binding. Therefore, these features may be related to the binding selectivity of the group III alpha-like toxins. The charge changes of residues 8, 10, 18, 28, 55 and 59 from neutral or negative to positive or neutral, which leads to a positive electrostatic potential surface, may be responsible for the high toxicity of BmK M2.


  • Organizational Affiliation

    Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (BMK M2)64Mesobuthus martensiiMutation(s): 0 
UniProt
Find proteins for P58488 (Mesobuthus martensii)
Explore P58488 
Go to UniProtKB:  P58488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58488
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.64α = 90
b = 37.31β = 90
c = 37.95γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
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: 2000-03-31
    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: 2014-04-09
    Changes: Database references
  • Version 1.4: 2019-11-20
    Changes: Database references
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description