Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 64, Part 2 (February 2008)

protein structure communications

Acta Cryst. (2008). F64, 70-76 [ doi:10.1107/S1744309107068236 ]

Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 Å resolution

F. L. Imai, K. Nagata, N. Yonezawa, M. Nakano and M. Tanokura

Abstract: S100A13 is a member of the S100 family of EF-hand-containing calcium-binding proteins. S100A13 plays an important role in the secretion of fibroblast growth factor-1 and interleukin 1 [alpha] , two pro-angiogenic factors released by the nonclassical endoplasmic reticulum/Golgi-independent secretory pathway. The X-ray crystal structure of human S100A13 at pH 7.5 was determined at 1.8 Å resolution. The structure was solved by molecular replacement and was refined to a final R factor of 19.0%. The structure revealed that human S100A13 exists as a homodimer with two calcium ions bound to each protomer. The protomer is composed of four [alpha] -helices ( [alpha] ₁- [alpha] ₄), which form a pair of EF-hand motifs. Dimerization occurs by hydrophobic interactions between helices [alpha] ₁ and [alpha] ₄ and by intermolecular hydrogen bonds between residues from helix [alpha] ₁ and the residues between [alpha] ₂ and [alpha] ₃ of both chains. Despite the high similarity of the backbone conformation in each protomer, the crystal structures of human S100A13 at pH 7.5 (this study) and at pH 6.0 [Li et al. (2007), Biochem. Biophys. Res. Commun. 356, 616-621] exhibit recognizable differences in the relative orientation (2.5°) of the protomers within the dimer and also remarkable differences in the side-chain conformations of several amino-acid residues.

PDB reference: 2egd

Keywords: human S100A13; calcium-binding proteins.