1iko: Difference between revisions

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-[[Image:1iko.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1iko", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1iko|  PDB=1iko  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN'''
+==CRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN==
+<StructureSection load='1iko' size='340' side='right'caption='[[1iko]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1iko]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKO 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]] 1.92&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1iko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iko OCA], [https://pdbe.org/1iko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iko RCSB], [https://www.ebi.ac.uk/pdbsum/1iko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iko ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EFNB2_MOUSE EFNB2_MOUSE] Cell surface transmembrane ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Binds to receptor tyrosine kinase including EPHA4, EPHA3 and EPHB4. Together with EPHB4 plays a central role in heart morphogenesis and angiogenesis through regulation of cell adhesion and cell migration. EPHB4-mediated forward signaling controls cellular repulsion and segregation from EFNB2-expressing cells. May play a role in constraining the orientation of longitudinally projecting axons.
+== 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/ik/1iko_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1iko ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Eph receptor tyrosine kinases and their membrane-associated ligands, the ephrins, are essential regulators of axon guidance, cell migration, segmentation, and angiogenesis. There are two classes of vertebrate ephrin ligands which have distinct binding specificities for their cognate receptors. Multimerization of the ligands is required for receptor activation, and ephrin ligands themselves signal intracellularly upon binding Eph receptors. We have determined the structure of the extracellular domain of mouse ephrin-B2. The ephrin ectodomain is an eight-stranded beta barrel with topological similarity to plant nodulins and phytocyanins. Based on the structure, we have identified potential surface determinants of Eph/ephrin binding specificity and a ligand dimerization region. The high sequence similarity among ephrin ectodomains indicates that all ephrins may be modeled upon the ephrin-B2 structure presented here.
-==Overview==
+Crystal structure of an ephrin ectodomain.,Toth J, Cutforth T, Gelinas AD, Bethoney KA, Bard J, Harrison CJ Dev Cell. 2001 Jul;1(1):83-92. PMID:11703926<ref>PMID:11703926</ref>
-Eph receptor tyrosine kinases and their membrane-associated ligands, the ephrins, are essential regulators of axon guidance, cell migration, segmentation, and angiogenesis. There are two classes of vertebrate ephrin ligands which have distinct binding specificities for their cognate receptors. Multimerization of the ligands is required for receptor activation, and ephrin ligands themselves signal intracellularly upon binding Eph receptors. We have determined the structure of the extracellular domain of mouse ephrin-B2. The ephrin ectodomain is an eight-stranded beta barrel with topological similarity to plant nodulins and phytocyanins. Based on the structure, we have identified potential surface determinants of Eph/ephrin binding specificity and a ligand dimerization region. The high sequence similarity among ephrin ectodomains indicates that all ephrins may be modeled upon the ephrin-B2 structure presented here.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IKO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKO OCA].
+</div>
+<div class="pdbe-citations 1iko" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of an ephrin ectodomain., Toth J, Cutforth T, Gelinas AD, Bethoney KA, Bard J, Harrison CJ, Dev Cell. 2001 Jul;1(1):83-92. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11703926 11703926]
+*[[Ephrin|Ephrin]]
+*[[Ephrin receptor 3D structures|Ephrin receptor 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Bard J]]
-[[Category: Bard, J.]]
+[[Category: Bethoney KA]]
-[[Category: Bethoney, K A.]]
+[[Category: Cutforth T]]
-[[Category: Cutforth, T.]]
+[[Category: Gelinas AD]]
-[[Category: Gelinas, A D.]]
+[[Category: Harrison CJ]]
-[[Category: Harrison, C J.]]
+[[Category: Toth J]]
-[[Category: Toth, J.]]
-[[Category: Glycosylation]]
-[[Category: Greek key]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:06:24 2008''