3ca5: Difference between revisions

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-[[Image:3ca5.png|left|200px]]
+==Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose==
+<StructureSection load='3ca5' size='340' side='right' caption='[[3ca5]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ca5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CA5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA5 FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AMG:ALPHA-METHYL-D-GALACTOSIDE'>AMG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c9z|3c9z]], [[3ca0|3ca0]], [[3ca1|3ca1]], [[3ca3|3ca3]], [[3ca4|3ca4]], [[3ca6|3ca6]], [[3cah|3cah]]</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ca5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca5 PDBsum]</span></td></tr>
+<table>
+== 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/ca/3ca5_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bark of elderberry (Sambucus nigra) contains a galactose (Gal)/N-acetylgalactosamine (GalNAc)-specific lectin (SNA-II) corresponding to slightly truncated B-chains of a genuine Type-II ribosome-inactivating protein (Type-II RIPs, SNA-V), found in the same species. The three-dimensional X-ray structure of SNA-II has been determined in two distinct crystal forms, hexagonal and tetragonal, at 1.90 A and 1.35 A, respectively. In both crystal forms, the SNA-II molecule folds into two linked betabeta-trefoil domains, with an overall conformation similar to that of the B-chains of ricin and other Type-II RIPs. Glycosylation is observed at four sites along the polypeptide chain, accounting for 14 saccharide units. The high-resolution structures of SNA-II in complex with Gal and five Gal-related saccharides (GalNAc, lactose, alphaalpha1-methylgalactose, fucose, and the carcinoma-specific Tn antigen) were determined at 1.55 A resolution or better. Binding is observed in two saccharide-binding sites for most of the sugars: a conserved aspartate residue interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the binding sites, additional interactions with the protein involve the O6 atom. Analytical gel filtration, small angle X-ray scattering studies and crystal packing analysis indicate that, although some oligomeric species are present, the monomeric species predominate in solution. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
-{{STRUCTURE_3ca5|  PDB=3ca5  |  SCENE=  }}
+Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.,Maveyraud L, Niwa H, Guillet V, Svergun DI, Konarev PV, Palmer RA, Peumans WJ, Rouge P, Van Damme EJ, Reynolds CD, Mourey L Proteins. 2008 Sep 17. PMID:18798567<ref>PMID:18798567</ref>
-===Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_18798567}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3ca5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CA5 OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:018798567</ref><references group="xtra"/>
 [[Category: Sambucus nigra]]
 [[Category: Maveyraud, L.]]