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[[Image:1j35.gif|left|200px]]
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{{STRUCTURE_1j35|  PDB=1j35  |  SCENE=  }}
'''Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein'''


==Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein==
<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.


==Overview==
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>
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==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1J35 is a [[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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J35 OCA].
</div>
<div class="pdbe-citations 1j35" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/12695512 12695512]
*[[Factor IX 3D structures|Factor IX 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bos taurus]]
[[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: Calcium ion]]
[[Category: Gla domain]]
[[Category: Magnesium ion]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:44:56 2008''

Latest revision as of 10:14, 25 October 2023

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding ProteinCrystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Structural highlights

1j35 is a 3 chain structure with sequence from Bos taurus and Protobothrops flavoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[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

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.

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[3]

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

See Also

References

  1. ↑ Shikamoto Y, Morita T, Fujimoto Z, Mizuno H. Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein. J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512 doi:10.1074/jbc.M300650200
  2. ↑ Atoda H, Ishikawa M, Yoshihara E, Sekiya F, Morita T. Blood coagulation factor IX-binding protein from the venom of Trimeresurus flavoviridis: purification and characterization. J Biochem. 1995 Nov;118(5):965-73. PMID:8749314
  3. ↑ Shikamoto Y, Morita T, Fujimoto Z, Mizuno H. Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein. J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512 doi:10.1074/jbc.M300650200

1j35, resolution 1.80Å

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