2qqk: Difference between revisions

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-[[Image:2qqk.jpg|left|200px]]
- {{Structure
+==Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab==
-|PDB= 2qqk |SIZE=350|CAPTION= <scene name='initialview01'>2qqk</scene>, resolution 2.750&Aring;
+<StructureSection load='2qqk' size='340' side='right'caption='[[2qqk]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>
+<table><tr><td colspan='2'>[[2qqk]] is a 3 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=2QQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQK FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75&#8491;</td></tr>
-|GENE= NRP2, VEGF165R2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqk OCA], [https://pdbe.org/2qqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qqk RCSB], [https://www.ebi.ac.uk/pdbsum/2qqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qqk ProSAT]</span></td></tr>
-|RELATEDENTRY=[[2qqi|2QQI]], [[2qqj|2QQJ]], [[2qql|2QQL]], [[2qqm|2QQM]], [[2qqn|2QQN]], [[2qqo|2QQO]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqk OCA], [http://www.ebi.ac.uk/pdbsum/2qqk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qqk RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/NRP2_HUMAN NRP2_HUMAN] High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.
+== 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/qq/2qqk_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=2qqk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Neuropilins (Nrps) are co-receptors for class 3 semaphorins and vascular endothelial growth factors and important for the development of the nervous system and the vasculature. The extracellular portion of Nrp is composed of two domains that are essential for semaphorin binding (a1a2), two domains necessary for VEGF binding (b1b2), and one domain critical for receptor dimerization (c). We report several crystal structures of Nrp1 and Nrp2 fragments alone and in complex with antibodies that selectively block either semaphorin or vascular endothelial growth factor (VEGF) binding. In these structures, Nrps adopt an unexpected domain arrangement in which the a2, b1, and b2 domains form a tightly packed core that is only loosely connected to the a1 domain. The locations of the antibody epitopes together with in vitro experiments indicate that VEGF and semaphorin do not directly compete for Nrp binding. Based upon our structural and functional data, we propose possible models for ligand binding to neuropilins.
-'''Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab'''
+Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding.,Appleton BA, Wu P, Maloney J, Yin J, Liang WC, Stawicki S, Mortara K, Bowman KK, Elliott JM, Desmarais W, Bazan JF, Bagri A, Tessier-Lavigne M, Koch AW, Wu Y, Watts RJ, Wiesmann C EMBO J. 2007 Nov 28;26(23):4902-12. Epub 2007 Nov 8. PMID:17989695<ref>PMID:17989695</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qqk" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Neuropilins (Nrps) are co-receptors for class 3 semaphorins and vascular endothelial growth factors and important for the development of the nervous system and the vasculature. The extracellular portion of Nrp is composed of two domains that are essential for semaphorin binding (a1a2), two domains necessary for VEGF binding (b1b2), and one domain critical for receptor dimerization (c). We report several crystal structures of Nrp1 and Nrp2 fragments alone and in complex with antibodies that selectively block either semaphorin or vascular endothelial growth factor (VEGF) binding. In these structures, Nrps adopt an unexpected domain arrangement in which the a2, b1, and b2 domains form a tightly packed core that is only loosely connected to the a1 domain. The locations of the antibody epitopes together with in vitro experiments indicate that VEGF and semaphorin do not directly compete for Nrp binding. Based upon our structural and functional data, we propose possible models for ligand binding to neuropilins.
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Neuropilin|Neuropilin]]
-==About this Structure==
+*[[3D structures of human antibody|3D structures of human antibody]]
-QQK 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=2QQK OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding., Appleton BA, Wu P, Maloney J, Yin J, Liang WC, Stawicki S, Mortara K, Bowman KK, Elliott JM, Desmarais W, Bazan JF, Bagri A, Tessier-Lavigne M, Koch AW, Wu Y, Watts RJ, Wiesmann C, EMBO J. 2007 Nov 28;26(23):4902-12. Epub 2007 Nov 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17989695 17989695]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Appleton, B A.]]
+[[Category: Appleton BA]]
-[[Category: Wiesmann, C.]]
+[[Category: Wiesmann C]]
-[[Category: alternative splicing]]
-[[Category: developmental protein]]
-[[Category: differentiation]]
-[[Category: glycoprotein]]
-[[Category: hormone]]
-[[Category: membrane]]
-[[Category: neurogenesis]]
-[[Category: phage-derived antibody]]
-[[Category: semaphorin receptor]]
-[[Category: signaling protein]]
-[[Category: transmembrane]]
-[[Category: vegf receptor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:52:13 2008''