2hns - Revision history

OCA at 16:37, 13 December 2023

2023-12-13T16:37:48Z

←Older revision		Revision as of 16:37, 13 December 2023
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	==Structure of the AAGU tetraloop==		==Structure of the AAGU tetraloop==
-	<StructureSection load='2hns' size='340' side='right'caption='[[2hns~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2hns' size='340' side='right'caption='[[2hns]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HNS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
-	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [https://pdbe.org/2hns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [https://www.ebi.ac.uk/pdbsum/2hns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hns ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [https://pdbe.org/2hns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [https://www.ebi.ac.uk/pdbsum/2hns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hns ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fourmy, F]]	+	[[Category: Fourmy F]]
-	[[Category: Gaudin, C]]	+	[[Category: Gaudin C]]
-	[[Category: Yoshizawa, S]]	+	[[Category: Yoshizawa S]]
-	~~[[Category: Hairpin]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Tetraloop~~]]	+

OCA at 11:10, 5 January 2022

2022-01-05T11:10:57Z

←Older revision		Revision as of 11:10, 5 January 2022
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	<StructureSection load='2hns' size='340' side='right'caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2hns' size='340' side='right'caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HNS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
-	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [~~http~~://pdbe.org/2hns PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hns PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hns ProSAT]</span></td></tr>	+	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [https://pdbe.org/2hns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [https://www.ebi.ac.uk/pdbsum/2hns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hns ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:12, 1 April 2020

2020-04-01T10:12:54Z

←Older revision		Revision as of 10:12, 1 April 2020
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	==Structure of the AAGU tetraloop==		==Structure of the AAGU tetraloop==
-	<StructureSection load='2hns' size='340' side='right' caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2hns' size='340' side='right'caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fourmy, F]]		[[Category: Fourmy, F]]
	[[Category: Gaudin, C]]		[[Category: Gaudin, C]]

OCA at 06:38, 27 June 2018

2018-06-27T06:38:53Z

←Older revision		Revision as of 06:38, 27 June 2018
Line 1:		Line 1:
		+
	==Structure of the AAGU tetraloop==		==Structure of the AAGU tetraloop==
	<StructureSection load='2hns' size='340' side='right' caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2hns' size='340' side='right' caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
-	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [http://pdbe.org/2hns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [http://www.ebi.ac.uk/pdbsum/2hns PDBsum]</span></td></tr>	+	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [http://pdbe.org/2hns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [http://www.ebi.ac.uk/pdbsum/2hns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hns ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:44, 10 September 2015

2015-09-10T08:44:44Z

←Older revision		Revision as of 08:44, 10 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
-	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [http://www.ebi.ac.uk/pdbsum/2hns PDBsum]</span></td></tr>	+	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [http://pdbe.org/2hns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [http://www.ebi.ac.uk/pdbsum/2hns PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 2hns" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:27, 16 January 2015

2015-01-16T08:27:04Z

←Older revision		Revision as of 08:27, 16 January 2015
Line 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fourmy, F.]]	+	[[Category: Fourmy, F]]
-	[[Category: Gaudin, C.]]	+	[[Category: Gaudin, C]]
-	[[Category: Yoshizawa, S.]]	+	[[Category: Yoshizawa, S]]
	[[Category: Hairpin]]		[[Category: Hairpin]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Tetraloop]]		[[Category: Tetraloop]]

OCA at 15:29, 12 October 2014

2014-10-12T15:29:18Z

←Older revision		Revision as of 15:29, 12 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2hns.~~png\|left\|200px~~]]	+	==Structure of the AAGU tetraloop==
		+	<StructureSection load='2hns' size='340' side='right' caption='[[2hns]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HNS FirstGlance]. <br>
		+	</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=2hns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hns OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hns RCSB], [http://www.ebi.ac.uk/pdbsum/2hns PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNase III enzymes are a highly conserved family of proteins that specifically cleave double-stranded RNA (dsRNA). These proteins are involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference. In yeast Rnt1p, a dsRNA-binding domain (dsRBD) recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops. The enzyme uses the tetraloop to cut 14nt to 16nt away into the stem in a ruler-like mechanism. The solution structure of Rnt1p dsRBD complexed to one of its small nucleolar (sno) RNA substrate revealed non-sequence-specific contacts with the sugar-phosphate backbone in the minor groove of the AGNN fold and the two non-conserved tetraloop nucleotides. Recently, a new form of Rnt1p substrates lacking the conserved AGNN sequence but instead harboring an AAGU tetraloop was found at the 5' end of snoRNA 48 precursor. Here, we report the solution structure of this hairpin capped with an AAGU tetraloop. Some of the stacking interactions and the position of the turn in the sugar-phosphate backbone are similar to the one observed in the AGNN loop structure; however, the AAGU sequence adopts a different conformation. The most striking difference was found at the 3' end of the loop where Rnt1p interacts with AGNN substrates. The last nucleotide is extruded from the AAGU tetraloop structure in contrast to the compact AGNN fold. The AAGU hairpin structure suggests that Rnt1p recognizes substrates with different tetraloop structures, indicating that the structural repertoire specifically recognized by Rnt1p is larger than previously anticipated.

-	~~{{STRUCTURE_2hns\| PDB=2hns \| SCENE= }}~~	+	Structure of an AAGU tetraloop and its contribution to substrate selection by yeast RNase III.,Gaudin C, Ghazal G, Yoshizawa S, Elela SA, Fourmy D J Mol Biol. 2006 Oct 20;363(2):322-31. Epub 2006 Aug 16. PMID:16979185<ref>PMID:16979185</ref>

-	~~===Structure~~ of the ~~AAGU tetraloop===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16979185}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[2hns]] is a 1 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA].~~	+	</StructureSection>
	[[Category: Fourmy, F.]]		[[Category: Fourmy, F.]]
	[[Category: Gaudin, C.]]		[[Category: Gaudin, C.]]

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

2013-01-07T14:32:00Z

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

←Older revision

Revision as of 14:32, 7 January 2013

OCA at 14:31, 7 January 2013

2013-01-07T14:31:58Z

←Older revision		Revision as of 14:31, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2hns.png\|left\|200px]]		[[Image:2hns.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hns", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2hns\| PDB=2hns \| SCENE= }}		{{STRUCTURE_2hns\| PDB=2hns \| SCENE= }}

	===Structure of the AAGU tetraloop===		===Structure of the AAGU tetraloop===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16979185}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16979185 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16979185}}		{{ABSTRACT_PUBMED_16979185}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA].	+	[[2hns]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA].
-		+
-	~~==Reference==~~	+
-	Structure of an AAGU tetraloop and its contribution to substrate selection by yeast RNase III., Gaudin C, Ghazal G, Yoshizawa S, Elela SA, Fourmy D, J Mol Biol. 2006 Oct 20;363(2):322-31. Epub 2006 Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16979185 16979185]	+
	[[Category: Fourmy, F.]]		[[Category: Fourmy, F.]]
	[[Category: Gaudin, C.]]		[[Category: Gaudin, C.]]
	[[Category: Yoshizawa, S.]]		[[Category: Yoshizawa, S.]]
	[[Category: Hairpin]]		[[Category: Hairpin]]
		+	[[Category: Rna]]
	[[Category: Tetraloop]]		[[Category: Tetraloop]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:52:15 2008''

OCA at 20:52, 27 July 2008

2008-07-27T20:52:16Z

←Older revision		Revision as of 20:52, 27 July 2008
Line 1:		Line 1:
-	[[Image:2hns.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2hns.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2hns\| PDB=2hns \| SCENE= }}		{{STRUCTURE_2hns\| PDB=2hns \| SCENE= }}

-	~~'''~~Structure of the AAGU tetraloop~~'''~~	+	===Structure of the AAGU tetraloop===


-	~~==Overview==~~	+	<!--
-	~~RNase III enzymes are a highly conserved family of proteins that specifically cleave double~~-~~stranded RNA (dsRNA). These proteins are involved in a variety of cellular functions, including the processing of many non~~-~~coding RNAs~~, ~~mRNA decay~~, ~~and RNA interference. In yeast Rnt1p, a dsRNA-binding domain (dsRBD) recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops. The enzyme uses~~ the ~~tetraloop to cut 14nt~~ to ~~16nt away into~~ the ~~stem in a ruler-like mechanism. The solution structure of Rnt1p dsRBD complexed to one of its small nucleolar~~ (sno) RNA substrate revealed non-sequence-specific contacts with the sugar-phosphate backbone in the minor groove of the AGNN fold and the two non-conserved tetraloop nucleotides. Recently, a new form of Rnt1p substrates lacking the conserved AGNN sequence but instead harboring an AAGU tetraloop was found at ~~the 5' end of snoRNA 48 precursor~~. ~~Here, we report the solution structure of this hairpin capped with an AAGU tetraloop~~. ~~Some of the stacking interactions and the position of the turn in the sugar-phosphate backbone are similar to the one observed in the AGNN loop structure; however~~, ~~the AAGU sequence adopts a different conformation. The most striking difference was found at the 3' end of the loop~~ where ~~Rnt1p interacts with AGNN substrates. The last nucleotide~~ is ~~extruded from~~ the AAGU tetraloop structure in contrast to the compact AGNN fold. The AAGU hairpin structure suggests that Rnt1p recognizes substrates with different tetraloop structures, indicating that the structural repertoire specifically recognized by Rnt1p is larger than previously anticipated.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16979185}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16979185 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16979185}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HNS OCA].

	==Reference==		==Reference==
Line 25:		Line 29:
	[[Category: Hairpin]]		[[Category: Hairpin]]
	[[Category: Tetraloop]]		[[Category: Tetraloop]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun ~~May 4 06~~:29:47 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:52:15 2008''