2p8n - Revision history

OCA at 10:57, 30 August 2023

2023-08-30T10:57:34Z

←Older revision		Revision as of 10:57, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2p8n' size='340' side='right'caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2p8n' size='340' side='right'caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADE:ADENINE'>ADE</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]] 1.94Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [https://pdbe.org/2p8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [https://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [https://pdbe.org/2p8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [https://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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 32:		Line 31:

	==See Also==		==See Also==
-	*[[Ricin\|Ricin]]	+	*[[Ricin 3D structures\|Ricin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Castor bean]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RRNA N-glycosylase~~]]	+	[[Category: Ricinus communis]]
-	[[Category: Carra~~, J H~~]]	+	[[Category: Carra JH]]
-	[[Category: Machiesky~~, L M~~]]	+	[[Category: Machiesky LM]]
-	[[Category: Mchugh~~, C A~~]]	+	[[Category: Mchugh CA]]
-	[[Category: Millard~~, C B~~]]	+	[[Category: Millard CB]]
-	[[Category: Mulligan, S]]	+	[[Category: Mulligan S]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: N-glycosidase]]~~	+
-	~~[[Category: Ricin]]~~	+
-	~~[[Category: Ricinus communi]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 07:55, 2 March 2022

2022-03-02T07:55:10Z

←Older revision		Revision as of 07:55, 2 March 2022
Line 3:		Line 3:
	<StructureSection load='2p8n' size='340' side='right'caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2p8n' size='340' side='right'caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2P8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=ADE:ADENINE'>ADE</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">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [~~http~~://pdbe.org/2p8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [https://pdbe.org/2p8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [https://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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]]

OCA at 08:10, 27 May 2020

2020-05-27T08:10:02Z

←Older revision		Revision as of 08:10, 27 May 2020
Line 1:		Line 1:

	==Ricin a-chain (recombinant) complex with adenine==		==Ricin a-chain (recombinant) complex with adenine==
-	<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='2p8n' size='340' side='right'caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2P8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=ADE:ADENINE'>ADE</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">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://pdbe.org/2p8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://pdbe.org/2p8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n 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: Carra, J H]]		[[Category: Carra, J H]]

OCA at 06:48, 22 August 2018

2018-08-22T06:48:42Z

←Older revision		Revision as of 06:48, 22 August 2018
Line 1:		Line 1:
		+
	==Ricin a-chain (recombinant) complex with adenine==		==Ricin a-chain (recombinant) complex with adenine==
	<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://pdbe.org/2p8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://pdbe.org/2p8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p8/2p8n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p8/2p8n_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 04:08, 10 February 2016

2016-02-10T04:08:41Z

←Older revision		Revision as of 04:08, 10 February 2016
Line 18:		Line 18:
	<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=2p8n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:14, 11 September 2015

2015-09-11T05:14:10Z

←Older revision		Revision as of 05:14, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=ADE:ADENINE'>ADE</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">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://pdbe.org/2p8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2p8n" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ricinus communis~~]]	+	[[Category: Castor bean]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Carra, J H]]		[[Category: Carra, J H]]

OCA at 11:41, 25 December 2014

2014-12-25T11:41:54Z

←Older revision		Revision as of 11:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n 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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n 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: Carra, J H.]]	+	[[Category: Carra, J H]]
-	[[Category: Machiesky, L M.]]	+	[[Category: Machiesky, L M]]
-	[[Category: Mchugh, C A.]]	+	[[Category: Mchugh, C A]]
-	[[Category: Millard, C B.]]	+	[[Category: Millard, C B]]
-	[[Category: Mulligan, S.]]	+	[[Category: Mulligan, S]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: N-glycosidase]]		[[Category: N-glycosidase]]

OCA at 07:19, 29 September 2014

2014-09-29T07:19:28Z

←Older revision		Revision as of 07:19, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2p8n.~~png~~\|~~left~~\|200px]]	+	==Ricin a-chain (recombinant) complex with adenine==
		+	<StructureSection load='2p8n' size='340' side='right' caption='[[2p8n]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2p8n]] 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=2P8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P8N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zb0\|1zb0]], [[1zam\|1zam]], [[1zb2\|1zb2]]</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=2p8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p8n RCSB], [http://www.ebi.ac.uk/pdbsum/2p8n 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/p8/2p8n_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 ==
		+	BACKGROUND: Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA) acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. RESULTS: We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a DeltaH of -13 +/- 2 kJ/mol and a DeltaS of -0.04 +/- 0.01 kJ/(K*mol). The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. CONCLUSION: We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding to a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.

-	~~{{STRUCTURE_2p8n\| PDB=2p8n \| SCENE= }}~~	+	Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site.,Carra JH, McHugh CA, Mulligan S, Machiesky LM, Soares AS, Millard CB BMC Struct Biol. 2007 Nov 6;7:72. PMID:17986339<ref>PMID:17986339</ref>

-	~~===Ricin~~ a~~-chain (recombinant) complex with adenine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17986339}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2p8n]] 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=2P8N OCA].~~	+

	==See Also==		==See Also==
	*[[Ricin\|Ricin]]		*[[Ricin\|Ricin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017986339<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]

OCA at 16:17, 20 October 2012

2012-10-20T16:17:01Z

←Older revision		Revision as of 16:17, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2p8n]] 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=2P8N OCA].	+	[[2p8n]] 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=2P8N OCA].

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

OCA: Protected "2p8n" [edit=sysop:move=sysop]

2012-07-26T21:10:24Z

Protected "2p8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:10, 26 July 2012