3ca6 - Revision history

OCA at 06:35, 3 April 2024

2024-04-03T06:35:26Z

←Older revision		Revision as of 06:35, 3 April 2024
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	<StructureSection load='3ca6' size='340' side='right'caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3ca6' size='340' side='right'caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ca6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.4Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [~~http~~://pdbe.org/3ca6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ca6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca6 ProSAT]</span></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=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [https://pdbe.org/3ca6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ca6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NIGB_SAMNI NIGB_SAMNI]] Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.	+	[https://www.uniprot.org/uniprot/NIGB_SAMNI NIGB_SAMNI] Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=3ca6 ConSurf].		</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=3ca6 ConSurf].
	<div style="clear:both"></div>		<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ca6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Agglutinin 3D structures\|Agglutinin 3D structures]]		*[[Agglutinin 3D structures\|Agglutinin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
-	[[Category: Maveyraud, L]]	+	[[Category: Maveyraud L]]
-	[[Category: Mourey, L]]	+	[[Category: Mourey L]]
-	~~[[Category: Beta-trefoil]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Ricin-b domain]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 10:25, 12 August 2020

2020-08-12T10:25:11Z

←Older revision		Revision as of 10:25, 12 August 2020
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	==Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen==		==Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen==
-	<StructureSection load='3ca6' size='340' side='right' caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='3ca6' size='340' side='right'caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT~~</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC~~</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://pdbe.org/3ca6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca6 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://pdbe.org/3ca6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Agglutinin\|Agglutinin]]	+	*[[Agglutinin 3D structures\|Agglutinin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
	[[Category: Maveyraud, L]]		[[Category: Maveyraud, L]]

OCA at 14:01, 7 November 2018

2018-11-07T14:01:02Z

←Older revision		Revision as of 14:01, 7 November 2018
Line 1:		Line 1:
		+
	==Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen==		==Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen==
	<StructureSection load='3ca6' size='340' side='right' caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3ca6' size='340' side='right' caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=~~NAG~~:N-~~ACETYL~~-~~D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~SER~~:~~SERINE~~'>~~SER~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~FUC~~:~~ALPHA-L-FUCOSE~~'>~~FUC~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://pdbe.org/3ca6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://pdbe.org/3ca6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/3ca6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/3ca6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3ca6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ca6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Agglutinin\|Agglutinin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:56, 9 February 2016

2016-02-09T22:56:33Z

←Older revision		Revision as of 22:56, 9 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://pdbe.org/3ca6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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].	+	</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=3ca6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3ca6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:06, 25 December 2014

2014-12-25T10:06:18Z

←Older revision		Revision as of 10:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[3cah\|3cah]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c9z\|3c9z]], [[3ca0\|3ca0]], [[3ca1\|3ca1]], [[3ca3\|3ca3]], [[3ca4\|3ca4]], [[3ca5\|3ca5]], [[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=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NIGB_SAMNI NIGB_SAMNI]] Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
-	[[Category: Maveyraud, L.]]	+	[[Category: Maveyraud, L]]
-	[[Category: Mourey, L.]]	+	[[Category: Mourey, L]]
	[[Category: Beta-trefoil]]		[[Category: Beta-trefoil]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]

OCA at 21:34, 2 October 2014

2014-10-02T21:34:11Z

←Older revision		Revision as of 21:34, 2 October 2014
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-	[[~~Image:~~3ca6.~~png~~\|~~left~~\|200px]]	+	==Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen==
		+	<StructureSection load='3ca6' size='340' side='right' caption='[[3ca6]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ca6]] 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=3CA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</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]], [[3ca5\|3ca5]], [[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=3ca6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ca6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca6 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/3ca6_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_3ca6\| PDB=3ca6 \| 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>

-	~~===Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18798567}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3ca6]] 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=3CA6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018798567<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
	[[Category: Maveyraud, L.]]		[[Category: Maveyraud, L.]]

OCA: Protected "3ca6" [edit=sysop:move=sysop]

2013-01-07T21:45:56Z

Protected "3ca6" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:45, 7 January 2013

OCA at 21:45, 7 January 2013

2013-01-07T21:45:50Z

←Older revision		Revision as of 21:45, 7 January 2013
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-	{{Seed}}
	[[Image:3ca6.png\|left\|200px]]		[[Image:3ca6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ca6", 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.
-	-->
	{{STRUCTURE_3ca6\| PDB=3ca6 \| SCENE= }}		{{STRUCTURE_3ca6\| PDB=3ca6 \| SCENE= }}

	===Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen===		===Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18798567}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18798567 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18798567}}		{{ABSTRACT_PUBMED_18798567}}

	==About this Structure==		==About this Structure==
-	~~3CA6~~ is a 1 chain structure of 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=3CA6 OCA].	+	[[3ca6]] 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=3CA6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18798567~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018798567</ref><references group="xtra"/>
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
	[[Category: Maveyraud, L.]]		[[Category: Maveyraud, L.]]
Line 34:		Line 22:
	[[Category: Ricin-b domain]]		[[Category: Ricin-b domain]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 10:29:26 2009''

OCA at 08:29, 22 March 2009

2009-03-22T08:29:28Z

←Older revision		Revision as of 08:29, 22 March 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3CA6 is a ~~[[Single protein]]~~ structure of 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=3CA6 OCA].	+	3CA6 is a 1 chain structure of 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=3CA6 OCA].

	==Reference==		==Reference==
-	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:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18798567 18798567]~~	+	<ref group="xtra">PMID:18798567</ref><references group="xtra"/>
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Maveyraud, L.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]	+	[[Category: Mourey, L.]]
	[[Category: Beta-trefoil]]		[[Category: Beta-trefoil]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
Line 35:		Line 35:
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Mar ~~18 20~~:29:01 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 10:29:26 2009''

OCA at 18:29, 18 March 2009

2009-03-18T18:29:02Z

←Older revision		Revision as of 18:29, 18 March 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3CA6 is a ~~1 chain~~ structure of 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=3CA6 OCA].	+	3CA6 is a [[Single protein]] structure of 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=3CA6 OCA].

	==Reference==		==Reference==
-	~~<ref group="xtra">~~PMID:~~18798567<~~/~~ref><references group="xtra"~~/>	+	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:[http://www.ncbi.nlm.nih.gov/pubmed/18798567 18798567]
	[[Category: Sambucus nigra]]		[[Category: Sambucus nigra]]
-	[[Category: ~~Maveyraud, L.~~]]	+	[[Category: Single protein]]
-	[[Category: ~~Mourey~~, L.]]	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
	[[Category: Beta-trefoil]]		[[Category: Beta-trefoil]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
Line 35:		Line 35:
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 18 20:12:48 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 18 20:29:01 2009''