1ifu - Revision history

OCA at 07:34, 7 February 2024

2024-02-07T07:34:55Z

←Older revision		Revision as of 07:34, 7 February 2024
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	<StructureSection load='1ifu' size='340' side='right'caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1ifu' size='340' side='right'caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMC:(1S)~~-~~1-(7-AMINO-1H-PYRAZOLO~~[~~4,3-D~~]~~PYRIMIDIN-3-YL)-1,~~4~~-ANHYDRO-D-RIBITOL'>FMC</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]] 2.4Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [https://pdbe.org/1ifu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [https://www.ebi.ac.uk/pdbsum/1ifu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifu 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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [https://pdbe.org/1ifu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [https://www.ebi.ac.uk/pdbsum/1ifu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifu 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]]
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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=1ifu 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=1ifu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ricin is a potent plant toxin which acts by removing a specific adenine residue from the ribosome. The X-ray crystal structure of a new, tetragonal crystal form of the recombinant ricin A-chain diffracting to 1.8 A resolution has been determined via molecular replacement methods and refined to a crystallographic R-factor of 18.6%. The higher resolution electron density allowed improvements to be made upon previously published models, resulting in an increase in the assigned secondary structure of the protein. The enzyme adopts the same global conformation in this crystal form with differences in detail due only partly to crystal packing. The active site superimposes closely with those of previously published models but the locations of the active-site water molecules differ in this structure. To address the current mechanistic model, an additional two structures are presented: recombinant ricin A-chain complexed with the substrate analogue formycin monophosphate as well as with adenosine monophosphate, which is cleaved by the crystalline enzyme. The formycin monophosphate displaces a putative catalytic water molecule. This supports the notion that the analogue does not bind in a transition state conformation and that contacts from other elements of the 28 S RNA natural substrate are required to achieve full reactivity. The structure of the adenosine monophosphate complex suggests a mechanism for the release of the adenine product via of the side-chain Tyr80. The structures suggest that Glu177 is better positioned for the activation of the catalytic water molecule than Arg180.
-
-	X-ray structure of recombinant ricin A-chain at 1.8 A resolution.,Weston SA, Tucker AD, Thatcher DR, Derbyshire DJ, Pauptit RA J Mol Biol. 1994 Dec 9;244(4):410-22. PMID:7990130<ref>PMID:7990130</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ifu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Ricin\|Ricin]]	+	*[[Ricin 3D structures\|Ricin 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Castor bean]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RRNA N-glycosylase~~]]	+	[[Category: Ricinus communis]]
-	[[Category: Derbyshire~~, D J~~]]	+	[[Category: Derbyshire DJ]]
-	[[Category: Pauptit~~, R A~~]]	+	[[Category: Pauptit RA]]
-	[[Category: Thatcher~~, D R~~]]	+	[[Category: Thatcher DR]]
-	[[Category: Tucker~~, A D~~]]	+	[[Category: Tucker AD]]
-	[[Category: Weston~~, S A]]~~	+	[[Category: Weston SA]]
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 11:00, 4 August 2021

2021-08-04T11:00:21Z

←Older revision		Revision as of 11:00, 4 August 2021
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	<StructureSection load='1ifu' size='340' side='right'caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1ifu' size='340' side='right'caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IFU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [~~http~~://pdbe.org/1ifu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ifu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifu 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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [https://pdbe.org/1ifu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [https://www.ebi.ac.uk/pdbsum/1ifu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifu 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 10:06, 30 October 2019

2019-10-30T10:06:20Z

←Older revision		Revision as of 10:06, 30 October 2019
Line 1:		Line 1:

	==RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN==		==RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN==
-	<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1ifu' size='340' side='right'caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ifu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ifu_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Castor bean]]		[[Category: Castor bean]]
		+	[[Category: Large Structures]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Derbyshire, D J]]		[[Category: Derbyshire, D J]]

OCA at 06:39, 29 November 2017

2017-11-29T06:39:44Z

←Older revision		Revision as of 06:39, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ifu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Castor bean]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Derbyshire, D J]]		[[Category: Derbyshire, D J]]

OCA at 10:50, 27 September 2017

2017-09-27T10:50:18Z

←Older revision		Revision as of 10:50, 27 September 2017
Line 1:		Line 1:
		+
	==RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN==		==RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN==
	<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ifu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://pdbe.org/1ifu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://pdbe.org/1ifu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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=1ifu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Castor bean]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Derbyshire, D J]]		[[Category: Derbyshire, D J]]

OCA at 10:37, 11 September 2015

2015-09-11T10:37:17Z

←Older revision		Revision as of 10:37, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://pdbe.org/1ifu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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 1ifu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ricinus communis~~]]	+	[[Category: Castor bean]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Derbyshire, D J]]		[[Category: Derbyshire, D J]]

OCA at 15:19, 25 December 2014

2014-12-25T15:19:10Z

←Older revision		Revision as of 15:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene></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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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 34:		Line 36:
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
-	[[Category: Derbyshire, D J.]]	+	[[Category: Derbyshire, D J]]
-	[[Category: Pauptit, R A.]]	+	[[Category: Pauptit, R A]]
-	[[Category: Thatcher, D R.]]	+	[[Category: Thatcher, D R]]
-	[[Category: Tucker, A D.]]	+	[[Category: Tucker, A D]]
-	[[Category: Weston, S A.]]	+	[[Category: Weston, S A]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Toxin]]		[[Category: Toxin]]

OCA at 08:33, 28 September 2014

2014-09-28T08:33:13Z

←Older revision		Revision as of 08:33, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ifu.~~png\|left~~\|200px]]	+	==RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN==
		+	<StructureSection load='1ifu' size='340' side='right' caption='[[1ifu]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ifu]] 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=1IFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene><br>
		+	<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=1ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ifu RCSB], [http://www.ebi.ac.uk/pdbsum/1ifu 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/if/1ifu_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 potent plant toxin which acts by removing a specific adenine residue from the ribosome. The X-ray crystal structure of a new, tetragonal crystal form of the recombinant ricin A-chain diffracting to 1.8 A resolution has been determined via molecular replacement methods and refined to a crystallographic R-factor of 18.6%. The higher resolution electron density allowed improvements to be made upon previously published models, resulting in an increase in the assigned secondary structure of the protein. The enzyme adopts the same global conformation in this crystal form with differences in detail due only partly to crystal packing. The active site superimposes closely with those of previously published models but the locations of the active-site water molecules differ in this structure. To address the current mechanistic model, an additional two structures are presented: recombinant ricin A-chain complexed with the substrate analogue formycin monophosphate as well as with adenosine monophosphate, which is cleaved by the crystalline enzyme. The formycin monophosphate displaces a putative catalytic water molecule. This supports the notion that the analogue does not bind in a transition state conformation and that contacts from other elements of the 28 S RNA natural substrate are required to achieve full reactivity. The structure of the adenosine monophosphate complex suggests a mechanism for the release of the adenine product via of the side-chain Tyr80. The structures suggest that Glu177 is better positioned for the activation of the catalytic water molecule than Arg180.

-	~~{{STRUCTURE_1ifu\| PDB=1ifu \| SCENE= }}~~	+	X-ray structure of recombinant ricin A-chain at 1.8 A resolution.,Weston SA, Tucker AD, Thatcher DR, Derbyshire DJ, Pauptit RA J Mol Biol. 1994 Dec 9;244(4):410-22. PMID:7990130<ref>PMID:7990130</ref>

-	~~===RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7990130}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ifu]] 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=1IFU OCA].~~	+

	==See Also==		==See Also==
	*[[Ricin\|Ricin]]		*[[Ricin\|Ricin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007990130<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ricinus communis]]		[[Category: Ricinus communis]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]

OCA at 18:14, 20 October 2012

2012-10-20T18:14:34Z

←Older revision		Revision as of 18:14, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ifu]] 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=1IFU OCA].	+	[[1ifu]] 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=1IFU OCA].

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

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

2012-07-27T03:27:20Z

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

←Older revision

Revision as of 03:27, 27 July 2012