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2egd
From Proteopedia
| 2egd, resolution 1.80Å () | |||||||||
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| Sites: | , , and | ||||||||
| Ligands: | |||||||||
| Gene: | S100A13 (Homo sapiens) | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal structure of human S100A13 in the Ca2+-bound state
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.
Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 A resolution., Imai FL, Nagata K, Yonezawa N, Nakano M, Tanokura M, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Feb 1;64(Pt, 2):70-6. Epub 2008 Jan 31. PMID:18259052
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2egd is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
- Imai FL, Nagata K, Yonezawa N, Nakano M, Tanokura M. Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Feb 1;64(Pt, 2):70-6. Epub 2008 Jan 31. PMID:18259052 doi:10.1107/S1744309107068236
- Imai FL, Nagata K, Yonezawa N, Yu J, Ito E, Kanai S, Tanokura M, Nakano M. Crystallization and preliminary X-ray analysis of human S100A13. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Nov 1;62(Pt, 11):1144-6. Epub 2006 Oct 20. PMID:17077500 doi:10.1107/S1744309106042473
