5yd0 - Revision history

OCA at 10:22, 27 March 2024

2024-03-27T10:22:50Z

←Older revision		Revision as of 10:22, 27 March 2024
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	==Crystal structure of Schlafen 13 (SLFN13) N'-domain==		==Crystal structure of Schlafen 13 (SLFN13) N'-domain==
-	<StructureSection load='5yd0' size='340' side='right' caption='[[5yd0]], [[Resolution\|resolution]] 3.18Å' scene=''>	+	<StructureSection load='5yd0' size='340' side='right'caption='[[5yd0]], [[Resolution\|resolution]] 3.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yd0]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yd0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YD0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ZN:ZINC+ION'>ZN</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]] 3.182Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Slfn13, Slfn8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10116 Buffalo rat])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd0 OCA], [~~http~~://pdbe.org/5yd0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yd0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yd0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd0 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=5yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd0 OCA], [https://pdbe.org/5yd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yd0 RCSB], [https://www.ebi.ac.uk/pdbsum/5yd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd0 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/SLN13_RAT SLN13_RAT] Endoribonuclease that cleaves tRNAs and rRNAs (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'-terminus at the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec) (PubMed:29563550).<ref>PMID:29563550</ref>
-	~~Cleavage of transfer (t)RNA and ribosomal (r)RNA are critical and conserved steps of translational control for cells to overcome varied environmental stresses~~. ~~However, enzymes that are responsible for this event have not been fully identified in high eukaryotes~~. ~~Here, we report a mammalian tRNA~~/~~rRNA-targeting endoribonuclease: SLFN13, a member of the Schlafen family. Structural study reveals a unique pseudo-dimeric U-pillow-shaped architecture of the SLFN13 N'-domain~~ that ~~may clamp base-paired RNAs. SLFN13 is able to digest~~ tRNAs and rRNAs ~~in vitro, and the endonucleolytic cleavage dissevers~~ 11 nucleotides from the 3'-terminus ~~of tRNA~~ at the acceptor stem. The cytoplasmically localised SLFN13 inhibits protein synthesis in 293T cells. Moreover, SLFN13 restricts HIV replication in a nucleolytic activity-dependent manner. According to these observations, we term SLFN13 RNase S13. Our study provides insights into the modulation of translational machinery in high eukaryotes, and sheds light on ~~the functional mechanisms of the Schlafen family.~~	+
-		+
-	~~Structure of Schlafen13 reveals a new class of~~ tRNA/rRNA- targeting RNase engaged in translational control.,Yang JY, Deng XY, Li YS, Ma XC, Feng JX, Yu B, Chen Y, Luo YL, Wang X, Chen ML, Fang ZX, Zheng FX, Li YP, Zhong Q, Kang TB, Song LB, Xu RH, Zeng MS, Chen W, Zhang H, Xie W, Gao S Nat Commun. 2018 Mar 21;9(1):~~1165~~. ~~doi: 10.1038/s41467-018-03544-x. PMID:29563550~~<ref>PMID:29563550</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yd0" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gao, S~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Yang, J Y~~]]	+	[[Category: Gao S]]
-	[[Category: ~~Anti~~-~~hiv]]~~	+	[[Category: Yang J-Y]]
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rrna]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 14:13, 11 April 2018

2018-04-11T14:13:51Z

←Older revision		Revision as of 14:13, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='5yd0' size='340' side='right' caption='[[5yd0]], [[Resolution\|resolution]] 3.18Å' scene=''>		<StructureSection load='5yd0' size='340' side='right' caption='[[5yd0]], [[Resolution\|resolution]] 3.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yd0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yd0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Slfn13, Slfn8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=5yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd0 OCA], [http://pdbe.org/5yd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yd0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd0 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=5yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd0 OCA], [http://pdbe.org/5yd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yd0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cleavage of transfer (t)RNA and ribosomal (r)RNA are critical and conserved steps of translational control for cells to overcome varied environmental stresses. However, enzymes that are responsible for this event have not been fully identified in high eukaryotes. Here, we report a mammalian tRNA/rRNA-targeting endoribonuclease: SLFN13, a member of the Schlafen family. Structural study reveals a unique pseudo-dimeric U-pillow-shaped architecture of the SLFN13 N'-domain that may clamp base-paired RNAs. SLFN13 is able to digest tRNAs and rRNAs in vitro, and the endonucleolytic cleavage dissevers 11 nucleotides from the 3'-terminus of tRNA at the acceptor stem. The cytoplasmically localised SLFN13 inhibits protein synthesis in 293T cells. Moreover, SLFN13 restricts HIV replication in a nucleolytic activity-dependent manner. According to these observations, we term SLFN13 RNase S13. Our study provides insights into the modulation of translational machinery in high eukaryotes, and sheds light on the functional mechanisms of the Schlafen family.
		+
		+	Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control.,Yang JY, Deng XY, Li YS, Ma XC, Feng JX, Yu B, Chen Y, Luo YL, Wang X, Chen ML, Fang ZX, Zheng FX, Li YP, Zhong Q, Kang TB, Song LB, Xu RH, Zeng MS, Chen W, Zhang H, Xie W, Gao S Nat Commun. 2018 Mar 21;9(1):1165. doi: 10.1038/s41467-018-03544-x. PMID:29563550<ref>PMID:29563550</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yd0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Gao, S]]		[[Category: Gao, S]]
	[[Category: Yang, J Y]]		[[Category: Yang, J Y]]

OCA at 06:35, 28 March 2018

2018-03-28T06:35:03Z

←Older revision		Revision as of 06:35, 28 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yd0 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Schlafen 13 (SLFN13) N'-domain==
-		+	<StructureSection load='5yd0' size='340' side='right' caption='[[5yd0]], [[Resolution\|resolution]] 3.18Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yd0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD0 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd0 OCA], [http://pdbe.org/5yd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yd0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gao, S]]
		+	[[Category: Yang, J Y]]
		+	[[Category: Anti-hiv]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rrna]]
		+	[[Category: Trna]]

OCA: Protected "5yd0" [edit=sysop:move=sysop]

2017-09-27T16:25:30Z

Protected "5yd0" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:25, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yd0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T16:25:29Z

New page: '''Unreleased structure''' The entry 5yd0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yd0 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]