1gqm: Difference between revisions

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-[[Image:1gqm.png|left|200px]]
-<!--
+==The structure of S100A12 in a hexameric form and its proposed role in receptor signalling==
-The line below this paragraph, containing "STRUCTURE_1gqm", creates the "Structure Box" on the page.
+<StructureSection load='1gqm' size='340' side='right'caption='[[1gqm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1gqm]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_1gqm|  PDB=1gqm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqm OCA], [https://pdbe.org/1gqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqm RCSB], [https://www.ebi.ac.uk/pdbsum/1gqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/S10AC_HUMAN S10AC_HUMAN] S100A12 is a calcium-, zinc- and copper-binding protein which plays a prominent role in the regulation of inflammatory processes and immune response. Its proinflammatory activity involves recruitment of leukocytes, promotion of cytokine and chemokine production, and regulation of leukocyte adhesion and migration. Acts as an alarmin or a danger associated molecular pattern (DAMP) molecule and stimulates innate immune cells via binding to receptor for advanced glycation endproducts (AGER). Binding to AGER activates the MAP-kinase and NF-kappa-B signaling pathways leading to production of proinflammatory cytokines and up-regulation of cell adhesion molecules ICAM1 and VCAM1. Acts as a monocyte and mast cell chemoattractant. Can stimulate mast cell degranulation and activation which generates chemokines, histamine and cytokines inducing further leukocyte recruitment to the sites of inflammation. Can inhibit the activity of matrix metalloproteinases; MMP2, MMP3 and MMP9 by chelating Zn(2+) from their active sites. Possesses filariacidal and filariastatic activity. Calcitermin possesses antifungal activity against C.albicans and is also active against E.coli and P.aeruginosa but not L.monocytogenes and S.aureus.<ref>PMID:11522286</ref> <ref>PMID:17208591</ref> <ref>PMID:18292089</ref> <ref>PMID:19386136</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gq/1gqm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gqm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+S100A12 is a member of the S100 subfamily of EF-hand calcium-binding proteins; it has been shown to be one of the ligands of the 'receptor for advanced glycation end products' (RAGE) that belongs to the immunoglobulin superfamily and is involved in diabetes, Alzheimer's disease, inflammation and tumour invasion. The structure of the dimeric form of native S100A12 from human granulocytes in the presence of calcium in space group R3 has previously been reported. Here, the structure of a second crystal form in space group P2(1) (unit-cell parameters a = 53.9, b = 100.5, c = 112.7A, beta = 94.6 degrees) solved at 2.7A resolution by molecular replacement using the R3 structure as a search model is reported. Like most S100 proteins, S100A12 is a dimer. However, in the P2(1) crystal form dimers of S100A12 are arranged in a spherical hexameric assembly with an external diameter of about 55 A stabilized by calcium ions bound between adjacent dimers. The putative target-binding sites of S100A12 are located at the outer surface of the hexamer, making it possible for the hexamer to bind several targets. It is proposed that the S100A12 hexameric assembly might interact with three extracellular domains of the receptor, bringing them together into large trimeric assemblies.
-===THE STRUCTURE OF S100A12 IN A HEXAMERIC FORM===
+The structure of S100A12 in a hexameric form and its proposed role in receptor signalling.,Moroz OV, Antson AA, Dodson EJ, Burrell HJ, Grist SJ, Lloyd RM, Maitland NJ, Dodson GG, Wilson KS, Lukanidin E, Bronstein IB Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):407-13. Epub 2002, Feb 21. PMID:11856825<ref>PMID:11856825</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gqm" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11856825}}, adds the Publication Abstract to the page
+*[[S100 proteins 3D structures|S100 proteins 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11856825 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11856825}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1gqm]] is a 12 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=1GQM OCA].
-==Reference==
-<ref group="xtra">PMID:11856825</ref><ref group="xtra">PMID:11134923</ref><ref group="xtra">PMID:10666601</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Antson, A A.]]
+[[Category: Large Structures]]
-[[Category: Bronstein, I B.]]
+[[Category: Antson AA]]
-[[Category: Burrel, H J.]]
+[[Category: Bronstein IB]]
-[[Category: Dodson, E G.]]
+[[Category: Burrel HJ]]
-[[Category: Dodson, G G.]]
+[[Category: Dodson EG]]
-[[Category: Grist, S J.]]
+[[Category: Dodson GG]]
-[[Category: Lloyd, R M.]]
+[[Category: Grist SJ]]
-[[Category: Lukanidin, E.]]
+[[Category: Lloyd RM]]
-[[Category: Maitland, N J.]]
+[[Category: Lukanidin E]]
-[[Category: Moroz, O V.]]
+[[Category: Maitland NJ]]
-[[Category: Wilson, K S.]]
+[[Category: Moroz OV]]
-[[Category: Calcium binding]]
+[[Category: Wilson KS]]
-[[Category: Ef-hand]]
-[[Category: S100 protein family]]
-[[Category: S100a12]]