1j35: Difference between revisions

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-[[Image:1j35.gif|left|200px]]<br /><applet load="1j35" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1j35, resolution 1.80&Aring;" />
-'''Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein'''<br />
-==Overview==
+==Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein==
-Factor IX is an indispensable protein required in the blood coagulation, cascade. It binds to the surface of phospholipid membrane by means of a, gamma-carboxyglutamic acid (Gla) domain situated at the N terminus., Recently, we showed that physiological concentrations of Mg2+ ions affect, the native conformation of the Gla domain and in doing so augment the, biological activity of factor IXa and binding affinity with its binding, protein even in the presence of Ca2+ ions. Here we report on the crystal, structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla, domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and, 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound, in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+, ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound, structures of the complexes showed that Mg2+ ion, which formed a bridge, between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative, to IX-bp and hence might be the cause of a more tight interaction between, the molecules than in the case of the Mg2+-free structure. The results, clearly suggest that Mg2+ ions are required to maintain native, conformation and in vivo function of factor IX Gla domain during blood, coagulation.
+<StructureSection load='1j35' size='340' side='right'caption='[[1j35]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j35]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Protobothrops_flavoviridis Protobothrops flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J35 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J35 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#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>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j35 OCA], [https://pdbe.org/1j35 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j35 RCSB], [https://www.ebi.ac.uk/pdbsum/1j35 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j35 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SLA_PROFL SLA_PROFL] Anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (F9) (but not factor X) in the presence of calcium with a 1 to 1 stoichiometry.<ref>PMID:12695512</ref> <ref>PMID:8749314</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/j3/1j35_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=1j35 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Factor IX is an indispensable protein required in the blood coagulation cascade. It binds to the surface of phospholipid membrane by means of a gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we showed that physiological concentrations of Mg2+ ions affect the native conformation of the Gla domain and in doing so augment the biological activity of factor IXa and binding affinity with its binding protein even in the presence of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg2+-free structure. The results clearly suggest that Mg2+ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.
-==About this Structure==
+Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein.,Shikamoto Y, Morita T, Fujimoto Z, Mizuno H J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512<ref>PMID:12695512</ref>
-J35 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Coagulation_factor_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J35 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein., Shikamoto Y, Morita T, Fujimoto Z, Mizuno H, J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12695512 12695512]
+</div>
+<div class="pdbe-citations 1j35" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Factor IX 3D structures|Factor IX 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Coagulation factor IXa]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Protobothrops flavoviridis]]
-[[Category: Trimeresurus flavoviridis]]
+[[Category: Fujimoto Z]]
-[[Category: Fujimoto, Z.]]
+[[Category: Mizuno H]]
-[[Category: Mizuno, H.]]
+[[Category: Morita T]]
-[[Category: Morita, T.]]
+[[Category: Shikamoto Y]]
-[[Category: Shikamoto, Y.]]
-[[Category: CA]]
-[[Category: calcium ion]]
-[[Category: gla domain]]
-[[Category: magnesium ion]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:53:46 2007''