PDBsum entry 1vb0

Toxin

PDB id: 1vb0

Contents

Protein chain

61 a.a. *

Ligands

SO4

TRS

Waters ×122

* Residue conservation analysis

PDB id:

1vb0

Name:

Toxin

Title:

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

Structure:

Cobrotoxin b. Chain: a. Synonym: cbt b, short neurotoxin, atratoxin-b

Source:

Naja atra. Chinese cobra. Organism_taxid: 8656

Resolution:

0.92Å R-factor: 0.114 R-free: 0.133

Authors:

X.Lou,Q.Liu,M.Teng,L.Niu,Q.Huang,Q.Hao

Key ref:

X.Lou et al. (2004). The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing. J Biol Chem, 279, 39094-39104. PubMed id: 15252034 DOI: 10.1074/jbc.M403863200

Date:

20-Feb-04 Release date: 21-Dec-04

Protein chain

P80958  (3S1CC_NAJAT) -  Cobrotoxin-b from Naja atra

Seq: 82 a.a.

Struc: 61 a.a.

DOI no: 10.1074/jbc.M403863200

J Biol Chem 279:39094-39104 (2004)

PubMed id: 15252034

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

X.Lou, Q.Liu, X.Tu, J.Wang, M.Teng, L.Niu, D.J.Schuller, Q.Huang, Q.Hao.

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.

Selected figure(s)

Figure 2.
FIG. 2. Dimeric representation of atratoxin linked by a Cu2+ ion in the asymmetric unit. Molecules A and B adopt a back-to-face orientation. Disulfide bonds are shown in brown and purple. Four residues chelated by a copper ion are colored in green and blue. All figures, if not specified, were prepared with Molscript (43) and O (33).

Figure 4.
FIG. 4. Anisotropic thermal motions of the two atratoxin molecules in the crystallographic asymmetric unit. These figures were prepared with RASTEP (35). The ellipsoids represent the moving directions of atoms. The colors are assigned based on B[eq] values. Atoms with lowest B[eq] are colored blue; atoms with highest B[eq] are colored red; and atoms between these are assigned color shading smoothly through a spectrum from dark blue to light red.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 39094-39104) copyright 2004.

Figures were selected by an automated process.