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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-1α, two pro-angiogenic factors released by the non-classical endoplasmic reticulum-Golgi-independent secretory pathway. To gain insight into the structural basis of the interactions with these proteins, we determined the crystal structure of human S100A13 at pH 7.5 at 1.8-Å resolution. Human S100A13 was heterologously expressed in Escherichia coli purified and crystallized by the hanging-drop vapor diffusion method using PEG 3350 as the precipitant and at pH 7.5. The crystals diffracted X-rays from a synchrotron-radiation source beyond 1.8-Å resolution. The crystal space group was assigned as primitive orthorhombic P212121 with unit-cell parameters a= 39.7Å, b= 59.2Å, c = 77.6Å. The structure was solved by molecular replacement and has been refined to a final R factor of 19.0% and a free R of 22.7%. The structure revealed that human S100A13 exists as a homodimer with two calcium ions bound to each protomer. The protomer is composed of 4 α-helices (α1-α4) forming a pair of EF-hand motifs. Dimerization occurs by hydrophobic interactions between helices α1 and α4 and by intermolecular hydrogen bonds between residues from helix α1 and the residues between α2 and α3 of both chains. Comparison between the crystal structures of human S100A13 at pH 7.5 (this study) and pH 6.0 (Li et al., 2007) exhibited recognizable differences in the relative orientation (ca. 2.5°) between the protomers within the dimer and also remarkable differences in the side-chain conformations of several amino-acid residues.

X-ray analysis of FliJ, a cytoplasmic component of the flagellar type III protein export apparatus