5j56 - Revision history

OCA at 12:36, 6 March 2024

2024-03-06T12:36:35Z

←Older revision		Revision as of 12:36, 6 March 2024
Line 10:		Line 10:
	== 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).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ricin toxin is a heterodimer consisting of RTA, a ribosome-inactivating protein, and RTB, a lectin that facilitates receptor-mediated uptake into mammalian cells. In previous studies, we demonstrated that toxin-neutralizing antibodies target four spatially distinct hotspots on RTA, which we refer to as epitope Clusters I-IV. In this report we identified and characterized three single domain camelid antibodies (VHH) against Cluster II. One of these VHHs, V5E1, ranks as one of the most potent ricin-neutralizing antibodies described to date. We solved the X-ray crystal structures of each of the three VHHs (E1, V1C7 and V5E1) in complex with RTA. V5E1 buries a total of 1,133 A2 of surface area on RTA and makes primary contacts with alpha-helix A (residues 18-32), alpha-helix F (182-194), as well as the F-G loop. V5E1, by virtue of complementary determining region 3 (CDR3), may also engage with RTB and potentially interfere with the high affinity galactose-recognition element that plays a critical role in toxin attachment to cell surfaces and intracellular trafficking. The two other VHHs, E1 and V1C7, bind epitopes adjacent to V5E1 but display only weak toxin-neutralizing activity, thereby providing the first structural insights into specific residues within Cluster II that may be critical contact points for toxin inactivation.
-
-	Structural analysis of single domain antibodies bound to a second neutralizing hot spot on ricin toxin's enzymatic subunit.,Rudolph MJ, Vance DJ, Cassidy MS, Rong Y, Mantis NJ J Biol Chem. 2016 Nov 30. pii: jbc.M116.758102. PMID:27903650<ref>PMID:27903650</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5j56" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[Ricin 3D structures\|Ricin 3D structures]]
	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]		*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:48, 6 September 2023

2023-09-06T10:48:44Z

←Older revision		Revision as of 10:48, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5j56' size='340' side='right'caption='[[5j56]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5j56' size='340' side='right'caption='[[5j56]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j56]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alpaca Alpaca~~] and [~~http~~://en.wikipedia.org/wiki/~~Castor_bean Castor bean~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J56 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j56]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J56 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j57\|5j57]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5j56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j56 OCA], [https://pdbe.org/5j56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j56 RCSB], [https://www.ebi.ac.uk/pdbsum/5j56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j56 ProSAT]</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=5j56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j56 OCA], [~~http~~://pdbe.org/5j56 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j56 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j56 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j56 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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[Ricin\|Ricin]]	+	*[[Ricin 3D structures\|Ricin 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpaca]]
-	[[Category: Castor bean]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RRNA N-glycosylase~~]]	+	[[Category: Ricinus communis]]
-	[[Category: ~~Rudolph, M J~~]]	+	[[Category: Vicugna pacos]]
-	[[Category: ~~Hydrolase-immune system complex]]~~	+	[[Category: Rudolph MJ]]
-	~~[[Category: Ricin]]~~	+
-	~~[[Category: Rta~~]]	+

OCA at 16:21, 11 December 2019

2019-12-11T16:21:01Z

←Older revision		Revision as of 16:21, 11 December 2019
Line 1:		Line 1:

	==RTA-V1C7==		==RTA-V1C7==
-	<StructureSection load='5j56' size='340' side='right' caption='[[5j56]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5j56' size='340' side='right'caption='[[5j56]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J56 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j57\|5j57]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j57\|5j57]]</td></tr>
Line 22:		Line 22:

	==See Also==		==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Ricin\|Ricin]]		*[[Ricin\|Ricin]]
	== References ==		== References ==
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alpaca]]
		+	[[Category: Castor bean]]
		+	[[Category: Large Structures]]
	[[Category: RRNA N-glycosylase]]		[[Category: RRNA N-glycosylase]]
	[[Category: Rudolph, M J]]		[[Category: Rudolph, M J]]

OCA at 07:21, 6 October 2017

2017-10-06T07:21:01Z

←Older revision		Revision as of 07:21, 6 October 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5j56" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j56" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ricin\|Ricin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:47, 22 December 2016

2016-12-22T14:47:42Z

←Older revision		Revision as of 14:47, 22 December 2016
Line 11:		Line 11:
	== 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).		[[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).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ricin toxin is a heterodimer consisting of RTA, a ribosome-inactivating protein, and RTB, a lectin that facilitates receptor-mediated uptake into mammalian cells. In previous studies, we demonstrated that toxin-neutralizing antibodies target four spatially distinct hotspots on RTA, which we refer to as epitope Clusters I-IV. In this report we identified and characterized three single domain camelid antibodies (VHH) against Cluster II. One of these VHHs, V5E1, ranks as one of the most potent ricin-neutralizing antibodies described to date. We solved the X-ray crystal structures of each of the three VHHs (E1, V1C7 and V5E1) in complex with RTA. V5E1 buries a total of 1,133 A2 of surface area on RTA and makes primary contacts with alpha-helix A (residues 18-32), alpha-helix F (182-194), as well as the F-G loop. V5E1, by virtue of complementary determining region 3 (CDR3), may also engage with RTB and potentially interfere with the high affinity galactose-recognition element that plays a critical role in toxin attachment to cell surfaces and intracellular trafficking. The two other VHHs, E1 and V1C7, bind epitopes adjacent to V5E1 but display only weak toxin-neutralizing activity, thereby providing the first structural insights into specific residues within Cluster II that may be critical contact points for toxin inactivation.
		+
		+	Structural analysis of single domain antibodies bound to a second neutralizing hot spot on ricin toxin's enzymatic subunit.,Rudolph MJ, Vance DJ, Cassidy MS, Rong Y, Mantis NJ J Biol Chem. 2016 Nov 30. pii: jbc.M116.758102. PMID:27903650<ref>PMID:27903650</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j56" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:14, 11 December 2016

2016-12-11T02:14:27Z

←Older revision		Revision as of 02:14, 11 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j56 is ~~ON HOLD until Paper Publication~~	+	==RTA-V1C7==
-		+	<StructureSection load='5j56' size='340' side='right' caption='[[5j56]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Rudolph~~, M.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J56 FirstGlance]. <br>
-	~~Description~~: ~~RTA~~-~~V1C7~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j57\|5j57]]</td></tr>
-	[[Category: Rudolph, M.J]]	+	<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=5j56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j56 OCA], [http://pdbe.org/5j56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j56 RCSB], [http://www.ebi.ac.uk/pdbsum/5j56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j56 ProSAT]</span></td></tr>
		+	</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).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RRNA N-glycosylase]]
		+	[[Category: Rudolph, M J]]
		+	[[Category: Hydrolase-immune system complex]]
		+	[[Category: Ricin]]
		+	[[Category: Rta]]

OCA at 15:03, 15 May 2016

2016-05-15T15:03:55Z

←Older revision		Revision as of 15:03, 15 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j56 is ON HOLD	+	The entry 5j56 is ON HOLD until Paper Publication

	Authors: Rudolph, M.J.		Authors: Rudolph, M.J.

OCA: Protected "5j56" [edit=sysop:move=sysop]

2016-05-11T01:28:42Z

Protected "5j56" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:28, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j56 is ON HOLD Authors: Rudolph, M.J. Description: RTA-V1C7 Category: Unreleased Structures Category: Rudolph, M.J

2016-05-11T01:28:41Z

New page: '''Unreleased structure''' The entry 5j56 is ON HOLD Authors: Rudolph, M.J. Description: RTA-V1C7 Category: Unreleased Structures Category: Rudolph, M.J

New page

'''Unreleased structure'''

The entry 5j56 is ON HOLD

Authors: Rudolph, M.J.

Description: RTA-V1C7
[[Category: Unreleased Structures]]
[[Category: Rudolph, M.J]]