1VB0

Atomic resolution structure of atratoxin-b, one short-chain neurotoxin from Naja atra

Summary for 1VB0

• Entry DOI: 10.2210/pdb1vb0/pdb
• Descriptor: Cobrotoxin b, SULFATE ION, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: short-chain neurotoxin, three-finger toxin, toxin
• Biological source: Naja atra (Chinese cobra)
• Cellular location: Secreted: P80958
• Total number of polymer chains: 1
• Total formula weight: 7061.89

Authors

Lou, X.,Liu, Q.,Teng, M.,Niu, L.,Huang, Q.,Hao, Q. (deposition date: 2004-02-20, release date: 2004-12-21, Last modification date: 2024-11-13)

Primary citation

Lou, X.,Liu, Q.,Tu, X.,Wang, J.,Teng, M.,Niu, L.,Schuller, D.J.,Huang, Q.,Hao, Q.
The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing
J.Biol.Chem., 279:39094-39104, 2004

PubMed Abstract: 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.

PubMed: 15252034
DOI: 10.1074/jbc.M403863200

Experimental method

X-RAY DIFFRACTION (0.92 Å)