1pum - Revision history

OCA at 05:59, 17 April 2024

2024-04-17T05:59:14Z

←Older revision		Revision as of 05:59, 17 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PUM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~GAL~~:BETA-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~FUL~~:~~BETA~~-L-~~FUCOSE~~'>~~FUL~~</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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]] 2.3Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1puu\|1puu]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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'>[https://proteopedia.org/fgij/fg.htm?mol=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [https://pdbe.org/1pum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [https://www.ebi.ac.uk/pdbsum/1pum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pum 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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [https://pdbe.org/1pum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [https://www.ebi.ac.uk/pdbsum/1pum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pum ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ML1_VISAL ML1_VISAL]] 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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15182350</ref> <ref>PMID:15001393</ref> <ref>PMID:1450445</ref>	+	[https://www.uniprot.org/uniprot/ML1_VISAL ML1_VISAL] 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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15182350</ref> <ref>PMID:15001393</ref> <ref>PMID:1450445</ref>
	== 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=1pum 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=1pum ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 A resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains alpha1 and gamma2 of the ML-I B-chain separated by approximately 62 A from each other. The favoured binding of galactose in subdomain alpha1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar-lectin complex. In the galactose-binding site II of subdomain gamma2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar-protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit beta1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.
-
-	Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.,Mikeska R, Wacker R, Arni R, Singh TP, Mikhailov A, Gabdoulkhakov A, Voelter W, Betzel C Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jan 1;61(Pt, 1):17-25. Epub 2004 Dec 24. PMID:16508080<ref>PMID:16508080</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pum" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Viscum album]]		[[Category: Viscum album]]
-	[[Category: Betzel, C]]	+	[[Category: Betzel C]]
-	[[Category: Konareva, N]]	+	[[Category: Konareva N]]
-	[[Category: Krauspenhaar, R]]	+	[[Category: Krauspenhaar R]]
-	[[Category: Mikhailov, A]]	+	[[Category: Mikhailov A]]
-	[[Category: Stoeva, S]]	+	[[Category: Stoeva S]]
-	[[Category: Voelter, W]]	+	[[Category: Voelter W]]
-	~~[[Category: Protein-sugar complex]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 09:35, 8 September 2021

2021-09-08T09:35:07Z

←Older revision		Revision as of 09:35, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1pum' size='340' side='right'caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pum' size='340' side='right'caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PUM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~FUL~~:BETA-L-~~FUCOSE~~'>~~FUL~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>, <scene name='pdbligand=~~NAG~~:N-~~ACETYL~~-~~D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG~~</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1puu\|1puu]]</div></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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [~~http~~://pdbe.org/1pum PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pum PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pum 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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [https://pdbe.org/1pum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [https://www.ebi.ac.uk/pdbsum/1pum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pum ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ML1_VISAL ML1_VISAL]] 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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15182350</ref> <ref>PMID:15001393</ref> <ref>PMID:1450445</ref>	+	[[https://www.uniprot.org/uniprot/ML1_VISAL ML1_VISAL]] 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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15182350</ref> <ref>PMID:15001393</ref> <ref>PMID:1450445</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:11, 27 November 2019

2019-11-27T10:11:18Z

←Older revision		Revision as of 10:11, 27 November 2019
Line 1:		Line 1:

	==Mistletoe lectin I in complex with galactose==		==Mistletoe lectin I in complex with galactose==
-	<StructureSection load='1pum' size='340' side='right' caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1pum' size='340' side='right'caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Viscum album]]		[[Category: Viscum album]]
	[[Category: Betzel, C]]		[[Category: Betzel, C]]

OCA at 08:11, 24 February 2018

2018-02-24T08:11:39Z

←Older revision		Revision as of 08:11, 24 February 2018
Line 1:		Line 1:
		+
	==Mistletoe lectin I in complex with galactose==		==Mistletoe lectin I in complex with galactose==
	<StructureSection load='1pum' size='340' side='right' caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pum' size='340' side='right' caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~GAL~~:BETA-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~FUL~~:~~BETA~~-L-~~FUCOSE~~'>~~FUL~~</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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">[[1puu\|1puu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://pdbe.org/1pum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum 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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://pdbe.org/1pum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pum 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/pu/1pum_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/1pum_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>
	</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=1pum ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:48, 11 September 2015

2015-09-11T07:48:46Z

←Older revision		Revision as of 07:48, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum 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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://pdbe.org/1pum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1pum" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:27, 25 December 2014

2014-12-25T13:27:12Z

←Older revision		Revision as of 13:27, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum 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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ML1_VISAL ML1_VISAL]] 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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15182350</ref> <ref>PMID:15001393</ref> <ref>PMID:1450445</ref>
	== 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: Viscum album]]		[[Category: Viscum album]]
-	[[Category: Betzel, C.]]	+	[[Category: Betzel, C]]
-	[[Category: Konareva, N.]]	+	[[Category: Konareva, N]]
-	[[Category: Krauspenhaar, R.]]	+	[[Category: Krauspenhaar, R]]
-	[[Category: Mikhailov, A.]]	+	[[Category: Mikhailov, A]]
-	[[Category: Stoeva, S.]]	+	[[Category: Stoeva, S]]
-	[[Category: Voelter, W.]]	+	[[Category: Voelter, W]]
	[[Category: Protein-sugar complex]]		[[Category: Protein-sugar complex]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 22:24, 28 September 2014

2014-09-28T22:24:25Z

←Older revision		Revision as of 22:24, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pum.~~png~~\|~~left~~\|200px]]	+	==Mistletoe lectin I in complex with galactose==
		+	<StructureSection load='1pum' size='340' side='right' caption='[[1pum]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PUM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1puu\|1puu]]</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=1pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pum OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pum RCSB], [http://www.ebi.ac.uk/pdbsum/1pum 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/pu/1pum_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 ==
		+	The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 A resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains alpha1 and gamma2 of the ML-I B-chain separated by approximately 62 A from each other. The favoured binding of galactose in subdomain alpha1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar-lectin complex. In the galactose-binding site II of subdomain gamma2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar-protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit beta1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.

-	~~{{STRUCTURE_1pum\| PDB=1pum \| SCENE= }}~~	+	Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.,Mikeska R, Wacker R, Arni R, Singh TP, Mikhailov A, Gabdoulkhakov A, Voelter W, Betzel C Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jan 1;61(Pt, 1):17-25. Epub 2004 Dec 24. PMID:16508080<ref>PMID:16508080</ref>

-	~~===Mistletoe lectin I in complex with galactose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16508080}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1pum]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Viscum_album Viscum album]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016508080<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Viscum album]]		[[Category: Viscum album]]
	[[Category: Betzel, C.]]		[[Category: Betzel, C.]]

OCA: Protected "1pum" [edit=sysop:move=sysop]

2012-12-19T11:44:37Z

Protected "1pum" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:44, 19 December 2012

OCA at 11:44, 19 December 2012

2012-12-19T11:44:34Z

←Older revision		Revision as of 11:44, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pum.png\|left\|200px]]		[[Image:1pum.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pum", 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_1pum\| PDB=1pum \| SCENE= }}		{{STRUCTURE_1pum\| PDB=1pum \| SCENE= }}

	===Mistletoe lectin I in complex with galactose===		===Mistletoe lectin I in complex with galactose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16508080}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16508080 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16508080}}		{{ABSTRACT_PUBMED_16508080}}

	==About this Structure==		==About this Structure==
-	~~1PUM~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA].	+	[[1pum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16508080~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016508080</ref><references group="xtra"/>
	[[Category: Viscum album]]		[[Category: Viscum album]]
	[[Category: Betzel, C.]]		[[Category: Betzel, C.]]
Line 32:		Line 20:
	[[Category: Voelter, W.]]		[[Category: Voelter, W.]]
	[[Category: Protein-sugar complex]]		[[Category: Protein-sugar complex]]
-		+	[[Category: Sugar binding protein]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:23:48 2009''~~	+

OCA at 15:23, 17 February 2009

2009-02-17T15:23:49Z

←Older revision		Revision as of 15:23, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA].	+	1PUM is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUM OCA].

	==Reference==		==Reference==
-	Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties., Mikeska R, Wacker R, Arni R, Singh TP, Mikhailov A, Gabdoulkhakov A, Voelter W, Betzel C, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jan 1;61(Pt, 1):17-25. Epub 2004 Dec 24. PMID:[~~http~~:~~//www.ncbi.nlm.nih.gov/pubmed/16508080 16508080~~]	+	<ref group="xtra">PMID:16508080</ref><references group="xtra"/>
		+	[[Category: Viscum album]]
	[[Category: Betzel, C.]]		[[Category: Betzel, C.]]
	[[Category: Konareva, N.]]		[[Category: Konareva, N.]]
Line 32:		Line 33:
	[[Category: Protein-sugar complex]]		[[Category: Protein-sugar complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:21:~~37 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:23:48 2009''