The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing

J Biol Chem. 2004 Sep 10;279(37):39094-104. doi: 10.1074/jbc.M403863200. Epub 2004 Jul 12.


By using single wavelength anomalous diffraction phasing based on the anomalous signal from copper atoms, the crystal structure of atratoxin was determined at the resolution of 1.5 A and was refined to an ultrahigh resolution of 0.87 A. The ultrahigh resolution electron density maps allowed the modeling of 38 amino acid residues in alternate conformations and the location of 322 of 870 possible hydrogen atoms. To get accurate information at the atomic level, atratoxin-b (an analog of atratoxin with reduced toxicity) was also refined to an atomic resolution of 0.92 A. By the sequence and structural comparison of these two atratoxins, Arg(33) and Arg(36) were identified to be critical to their varied toxicity. The effect of copper ions on the distribution of hydrogen atoms in atratoxin was discussed, and the interactions between copper ions and protein residues were analyzed based on a statistical method, revealing a novel pentahedral copper-binding motif.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Anisotropy
  • Base Sequence
  • Cloning, Molecular
  • Copper / chemistry
  • Crystallography, X-Ray
  • DNA, Complementary / metabolism
  • Databases as Topic
  • Elapid Venoms
  • Electrons
  • Hydrogen / chemistry
  • Insect Proteins
  • Ions
  • Models, Molecular
  • Molecular Sequence Data
  • Neurotoxins / chemistry*
  • Polymerase Chain Reaction
  • Protein Binding
  • Protein Conformation
  • Scorpion Venoms / metabolism
  • Sequence Homology, Amino Acid


  • DNA, Complementary
  • Elapid Venoms
  • Insect Proteins
  • Ions
  • Neurotoxins
  • Scorpion Venoms
  • atratoxin-b
  • Copper
  • Hydrogen

Associated data

  • GENBANK/AY471578
  • GENBANK/AY471579