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2egd

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Revision as of 22:32, 9 September 2015

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

Structural highlights

2egd is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	S100A13 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[S10AD_HUMAN] Plays a role in the export of proteins that lack a signal peptide and are secreted by an alternative pathway. Binds two calcium ions per subunit. Binds one copper ion. Binding of one copper ion does not interfere with calcium binding. Required for the copper-dependent stress-induced export of IL1A and FGF1. The calcium-free protein binds to lipid vesicles containing phosphatidylserine, but not to vesicles containing phosphatidylcholine (By similarity).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mandinova A, Soldi R, Graziani I, Bagala C, Bellum S, Landriscina M, Tarantini F, Prudovsky I, Maciag T. S100A13 mediates the copper-dependent stress-induced release of IL-1alpha from both human U937 and murine NIH 3T3 cells. J Cell Sci. 2003 Jul 1;116(Pt 13):2687-96. Epub 2003 May 13. PMID:12746488 doi:http://dx.doi.org/10.1242/jcs.00471
↑ Cao R, Yan B, Yang H, Zu X, Wen G, Zhong J. Effect of human S100A13 gene silencing on FGF-1 transportation in human endothelial cells. J Formos Med Assoc. 2010 Sep;109(9):632-40. doi: 10.1016/S0929-6646(10)60103-9. PMID:20863990 doi:http://dx.doi.org/10.1016/S0929-6646(10)60103-9
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2egd"

@@ Line 2: / Line 2: @@
 <StructureSection load='2egd' size='340' side='right' caption='[[2egd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2egd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EGD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2egd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EGD FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">S100A13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">S100A13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2egd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2egd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2egd RCSB], [http://www.ebi.ac.uk/pdbsum/2egd PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2egd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2egd OCA], [http://pdbe.org/2egd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2egd RCSB], [http://www.ebi.ac.uk/pdbsum/2egd PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2egd" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Imai, F L]]
 [[Category: Nagata, K]]

2egd

From Proteopedia

Revision as of 22:32, 9 September 2015

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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