2EGD

Crystal structure of human S100A13 in the Ca2+-bound state

Summary for 2EGD

• Entry DOI: 10.2210/pdb2egd/pdb
• Descriptor: Protein S100-A13, CALCIUM ION (3 entities in total)
• Functional Keywords: ef-hand, metal binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q99584
• Total number of polymer chains: 2
• Total formula weight: 23140.70

Authors

Imai, F.L.,Nagata, K.,Yonezawa, N.,Nakano, M.,Tanokura, M. (deposition date: 2007-02-28, release date: 2008-03-11, Last modification date: 2023-10-25)

Primary citation

Imai, F.L.,Nagata, K.,Yonezawa, N.,Nakano, M.,Tanokura, M.
Crystal structure of human S100A13 in the Ca2+-bound state
Acta Crystallogr.,Sect.F, 64:70-76, 2008

PubMed 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 A 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 ( approximately 2.5 degrees) of the protomers within the dimer and also remarkable differences in the side-chain conformations of several amino-acid residues.

PubMed: 18259052
DOI: 10.1107/S1744309107068236

Experimental method

X-RAY DIFFRACTION (1.8 Å)