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1edm

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[[Image:1edm.gif|left|200px]]
 
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{{Structure
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==EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX==
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|PDB= 1edm |SIZE=350|CAPTION= <scene name='initialview01'>1edm</scene>, resolution 1.5&Aring;
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<StructureSection load='1edm' size='340' side='right'caption='[[1edm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
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<table><tr><td colspan='2'>[[1edm]] is a 2 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=1EDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EDM FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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|GENE= HUMAN FACTOR IX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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<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>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1edm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1edm OCA], [https://pdbe.org/1edm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1edm RCSB], [https://www.ebi.ac.uk/pdbsum/1edm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1edm ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[https://omim.org/entry/306900 306900]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref> Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[https://omim.org/entry/300807 300807]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ed/1edm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1edm ConSurf].
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<div style="clear:both"></div>
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'''EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX'''
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==See Also==
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*[[Factor IX 3D structures|Factor IX 3D structures]]
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== References ==
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==Overview==
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<references/>
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Various diverse extracellular proteins possess Ca(2+)-binding epidermal growth factor (EGF)-like domains, the function of which remains uncertain. We have determined, at high resolution (1.5 A), the crystal structure of such a domain, from human clotting factor IX, as a complex with Ca2+. The Ca2+ ligands form a classic pentagonal bipyramid with six ligands contributed by one polypeptide chain and the seventh supplied by a neighboring EGF-like domain. The crystal structure identifies the role of Ca2+ in maintaining the conformation of the N-terminal region of the domain, but more importantly demonstrates that Ca2+ can directly mediate protein-protein contacts. The observed crystal packing of the domains provides a plausible model for the association of multiple tandemly linked EGF-like domains in proteins such as fibrillin-1, Notch, and protein S. This model is consistent with the known functional data and suggests a general biological role for these domains.
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__TOC__
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</StructureSection>
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==Disease==
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Known diseases associated with this structure: Hemophilia B OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=306900 306900]], Warfarin sensitivity OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=306900 306900]]
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==About this Structure==
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1EDM is a [[Single protein]] structure of 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=1EDM OCA].
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==Reference==
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The structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein-protein interactions., Rao Z, Handford P, Mayhew M, Knott V, Brownlee GG, Stuart D, Cell. 1995 Jul 14;82(1):131-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7606779 7606779]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Brownlee, G G.]]
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[[Category: Brownlee GG]]
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[[Category: Handford, P.]]
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[[Category: Handford P]]
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[[Category: Knott, V.]]
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[[Category: Knott V]]
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[[Category: Mayhew, M.]]
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[[Category: Mayhew M]]
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[[Category: Rao, Z.]]
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[[Category: Rao Z]]
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[[Category: Stuart, D.]]
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[[Category: Stuart D]]
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[[Category: CA]]
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[[Category: calcium-binding]]
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[[Category: coagulation factor]]
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[[Category: crystal structure]]
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[[Category: egf]]
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[[Category: egf-like domain]]
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[[Category: epidermal growth factor]]
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[[Category: human factor ix]]
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[[Category: structure and function]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:54:09 2008''
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Current revision

EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX

PDB ID 1edm

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