2vc3 - Revision history

OCA at 15:14, 13 December 2023

OCA — Wed, 13 Dec 2023 15:14:17 GMT

←Older revision		Revision as of 15:14, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2vc3' size='340' side='right'caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2vc3' size='340' side='right'caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Castor_bean Castor bean~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22]~~ </~~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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [https://pdbe.org/2vc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [https://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [https://pdbe.org/2vc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [https://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO]] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).	+	[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Castor bean]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RRNA N-glycosylase~~]]	+	[[Category: Ricinus communis]]
-	[[Category: Fulop, V]]	+	[[Category: Fulop V]]
-	[[Category: Marsden~~, C J]]~~	+	[[Category: Marsden CJ]]
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Plant defense]]~~	+
-	~~[[Category: Protein synthesis inhibitor]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 11:33, 30 March 2022

OCA — Wed, 30 Mar 2022 11:33:51 GMT

←Older revision		Revision as of 11:33, 30 March 2022
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	<StructureSection load='2vc3' size='340' side='right'caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2vc3' size='340' side='right'caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=ACT:ACETATE+ION'>ACT</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">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [~~http~~://pdbe.org/2vc3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [https://pdbe.org/2vc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [https://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO]] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).	+	[[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO]] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Ricin\|Ricin]]	+	*[[Ricin 3D structures\|Ricin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:43, 25 June 2020

OCA — Thu, 25 Jun 2020 07:43:18 GMT

←Older revision		Revision as of 07:43, 25 June 2020
Line 1:		Line 1:

	==Ricin A-Chain (Recombinant) E177D Mutant with a bound acetate==		==Ricin A-Chain (Recombinant) E177D Mutant with a bound acetate==
-	<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2vc3' size='340' side='right'caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=ACT:ACETATE+ION'>ACT</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">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://pdbe.org/2vc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://pdbe.org/2vc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Castor bean]]		[[Category: Castor bean]]
		+	[[Category: Large Structures]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Fulop, V]]		[[Category: Fulop, V]]

OCA at 21:08, 19 September 2018

OCA — Wed, 19 Sep 2018 21:08:08 GMT

←Older revision		Revision as of 21:08, 19 September 2018
Line 1:		Line 1:

-	==~~RICIN~~ A-~~CHAIN~~ (~~RECOMBINANT~~) E177D ~~MUTANT WITH A BOUND ACETATE~~==	+	==Ricin A-Chain (Recombinant) E177D Mutant with a bound acetate==
	<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/2vc3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/2vc3_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>

OCA at 10:01, 5 August 2016

OCA — Fri, 05 Aug 2016 10:01:03 GMT

←Older revision		Revision as of 10:01, 5 August 2016
Line 1:		Line 1:
		+
	==RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE==		==RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE==
	<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Ricinus_communis Ricinus communis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://pdbe.org/2vc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=2vc3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 2vc3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ricinus communis~~]]	+	[[Category: Castor bean]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Fulop, V]]		[[Category: Fulop, V]]

OCA at 17:53, 25 December 2014

OCA — Thu, 25 Dec 2014 17:53:22 GMT

←Older revision		Revision as of 17:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC3 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=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO]] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
-	[[Category: Fulop, V.]]	+	[[Category: Fulop, V]]
-	[[Category: Marsden, C J.]]	+	[[Category: Marsden, C J]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]

OCA at 07:55, 29 September 2014

OCA — Mon, 29 Sep 2014 07:55:25 GMT

←Older revision		Revision as of 07:55, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2vc3.~~png~~\|~~left~~\|200px]]	+	==RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE==
		+	<StructureSection load='2vc3' size='340' side='right' caption='[[2vc3]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC3 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=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1apg\|1apg]], [[1br5\|1br5]], [[1br6\|1br6]], [[1j1m\|1j1m]], [[1obs\|1obs]], [[1obt\|1obt]], [[1uq4\|1uq4]], [[1zam\|1zam]], [[1zb2\|1zb2]], [[2aai\|2aai]], [[1fmp\|1fmp]], [[1ifs\|1ifs]], [[1ift\|1ift]], [[1ifu\|1ifu]], [[1il3\|1il3]], [[1il4\|1il4]], [[1il5\|1il5]], [[1il9\|1il9]], [[1rtc\|1rtc]], [[1uq5\|1uq5]], [[1zb0\|1zb0]], [[2vc4\|2vc4]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></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=2vc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vc3 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc3 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/vc/2vc3_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 ==
		+	Ricin is a heterodimeric plant protein that is potently toxic to mammalian cells. Toxicity results from the catalytic depurination of eukaryotic ribosomes by ricin toxin A chain (RTA) that follows toxin endocytosis to, and translocation across, the endoplasmic reticulum membrane. To ultimately identify proteins required for these later steps in the entry process, it will be useful to express the catalytic subunit within the endoplasmic reticulum of yeast cells in a manner that initially permits cell growth. A subsequent switch in conditions to provoke innate toxin action would permit only those strains containing defects in genes normally essential for toxin retro-translocation, refolding or degradation to survive. As a route to such a screen, several RTA mutants with reduced catalytic activity have previously been isolated. Here we report the use of Saccharomyces cerevisiae to isolate temperature-dependent mutants of endoplasmic reticulum-targeted RTA. Two such toxin mutants with opposing phenotypes were isolated. One mutant RTA (RTAF108L/L151P) allowed the yeast cells that express it to grow at 37 degrees C, whereas the same cells did not grow at 23 degrees C. Both mutations were required for temperature-dependent growth. The second toxin mutant (RTAE177D) allowed cells to grow at 23 degrees C but not at 37 degrees C. Interestingly, RTAE177D has been previously reported to have reduced catalytic activity, but this is the first demonstration of a temperature-sensitive phenotype. To provide a more detailed characterization of these mutants we have investigated their N-glycosylation, stability, catalytic activity and, where appropriate, a three-dimensional structure. The potential utility of these mutants is discussed.

-	~~{{STRUCTURE_2vc3\| PDB=2vc3 \| SCENE= }}~~	+	The isolation and characterization of temperature-dependent ricin A chain molecules in Saccharomyces cerevisiae.,Allen SC, Moore KA, Marsden CJ, Fulop V, Moffat KG, Lord JM, Ladds G, Roberts LM FEBS J. 2007 Nov;274(21):5586-99. Epub 2007 Oct 4. PMID:17916187<ref>PMID:17916187</ref>

-	~~===RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17916187}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2vc3]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Ricinus_communis Ricinus communis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA].~~	+

	==See Also==		==See Also==
	*[[Ricin\|Ricin]]		*[[Ricin\|Ricin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017916187<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]

OCA at 19:40, 20 October 2012

OCA — Sat, 20 Oct 2012 19:40:19 GMT

←Older revision		Revision as of 19:40, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2vc3]] is a 1 chain structure ~~of [[Ricin]]~~ with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA].	+	[[2vc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA].

	==See Also==		==See Also==

OCA: Protected "2vc3" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 08:06:37 GMT

Protected "2vc3" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:06, 27 July 2012

OCA at 08:06, 27 July 2012

OCA — Fri, 27 Jul 2012 08:06:36 GMT

←Older revision		Revision as of 08:06, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2vc3.png\|left\|200px]]		[[Image:2vc3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2vc3", 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_2vc3\| PDB=2vc3 \| SCENE= }}		{{STRUCTURE_2vc3\| PDB=2vc3 \| SCENE= }}

	===RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE===		===RICIN A-CHAIN (RECOMBINANT) E177D MUTANT WITH A BOUND ACETATE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17916187}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17916187 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17916187}}		{{ABSTRACT_PUBMED_17916187}}

	==About this Structure==		==About this Structure==
-	~~2VC3~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA].	+	[[2vc3]] is a 1 chain structure of [[Ricin]] with sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC3 OCA].
		+
		+	==See Also==
		+	*[[Ricin\|Ricin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17916187~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017916187</ref><references group="xtra"/>
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
Line 35:		Line 26:
	[[Category: Protein synthesis inhibitor]]		[[Category: Protein synthesis inhibitor]]
	[[Category: Toxin]]		[[Category: Toxin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:45:05 2009''