1wks - Revision history

OCA at 09:28, 6 December 2023

2023-12-06T09:28:16Z

←Older revision		Revision as of 09:28, 6 December 2023
Line 1:		Line 1:

	==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==		==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==
-	<StructureSection load='1wks' size='340' side='right'caption='[[1wks~~]], [[NMR_Ensembles_of_Models \| 21 NMR models~~]]' scene=''>	+	<StructureSection load='1wks' size='340' side='right'caption='[[1wks]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKS 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [https://pdbe.org/1wks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [https://www.ebi.ac.uk/pdbsum/1wks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wks 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [https://pdbe.org/1wks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [https://www.ebi.ac.uk/pdbsum/1wks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wks 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: Baba, S]]	+	[[Category: Baba S]]
-	[[Category: Kajikawa, M]]	+	[[Category: Kajikawa M]]
-	[[Category: Kawai, G]]	+	[[Category: Kawai G]]
-	[[Category: Okada, N]]	+	[[Category: Okada N]]
-	~~[[Category: Line]]~~	+
-	~~[[Category: Pentaloop]]~~	+
-	~~[[Category: Retrotransposition]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 16:20, 27 October 2021

2021-10-27T16:20:38Z

←Older revision		Revision as of 16:20, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1wks' size='340' side='right'caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>		<StructureSection load='1wks' size='340' side='right'caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WKS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKS 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [~~http~~://pdbe.org/1wks PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wks PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wks 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [https://pdbe.org/1wks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [https://www.ebi.ac.uk/pdbsum/1wks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wks ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:54, 22 January 2020

2020-01-22T17:54:55Z

←Older revision		Revision as of 17:54, 22 January 2020
Line 1:		Line 1:

	==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==		==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==
-	<StructureSection load='1wks' size='340' side='right' caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>	+	<StructureSection load='1wks' size='340' side='right'caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
	[[Category: Kajikawa, M]]		[[Category: Kajikawa, M]]

OCA at 16:37, 11 April 2018

2018-04-11T16:37:16Z

←Older revision		Revision as of 16:37, 11 April 2018
Line 1:		Line 1:
		+
	==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==		==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==
	<StructureSection load='1wks' size='340' side='right' caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>		<StructureSection load='1wks' size='340' side='right' caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [http://pdbe.org/1wks PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [http://www.ebi.ac.uk/pdbsum/1wks 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [http://pdbe.org/1wks PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [http://www.ebi.ac.uk/pdbsum/1wks PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wks ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:20, 11 September 2015

2015-09-11T16:20:42Z

←Older revision		Revision as of 16:20, 11 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [http://www.ebi.ac.uk/pdbsum/1wks 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [http://pdbe.org/1wks PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [http://www.ebi.ac.uk/pdbsum/1wks 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 1wks" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:28, 15 January 2015

2015-01-15T18:28:25Z

←Older revision		Revision as of 18:28, 15 January 2015
Line 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baba, S.]]	+	[[Category: Baba, S]]
-	[[Category: Kajikawa, M.]]	+	[[Category: Kajikawa, M]]
-	[[Category: Kawai, G.]]	+	[[Category: Kawai, G]]
-	[[Category: Okada, N.]]	+	[[Category: Okada, N]]
	[[Category: Line]]		[[Category: Line]]
	[[Category: Pentaloop]]		[[Category: Pentaloop]]
	[[Category: Retrotransposition]]		[[Category: Retrotransposition]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 08:28, 8 October 2014

2014-10-08T08:28:03Z

←Older revision		Revision as of 08:28, 8 October 2014
Line 1:		Line 1:
-	[[~~Image~~:1wks.~~png\|left\|200px~~]]	+	==Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2==
		+	<StructureSection load='1wks' size='340' side='right' caption='[[1wks]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKS 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=1wks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wks OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wks RCSB], [http://www.ebi.ac.uk/pdbsum/1wks PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail containing a stem-loop that is critical for their retrotransposition. Presumably, the first step of retrotransposition is the recognition of their 3' tails by UnaL2-encoded reverse transcriptase. The solution structure of a 17-nucleotide RNA derived from the 3' tail of UnaL2 was determined by NMR. The GGAUA loop forms a specific structure in which the uridine is exposed to solvent with the third and fifth adenosines stacked. A sharp turn in the phosphodiester backbone occurs between the second guanosine and third adenosine. When the uridine is mutated (but not deleted), all mutants form the loop structure, indicating that the loop structure requires an exposed fourth residue. The retrotransposition assay in HeLa cells revealed that retrotransposition requires the second guanosine, although any nucleoside functions at the fourth position, suggesting that UnaL2 reverse transcriptase specifically recognizes the 5' side of the GGANA loop.

-	~~{{STRUCTURE_1wks\| PDB=1wks \| SCENE= }}~~	+	Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.,Baba S, Kajikawa M, Okada N, Kawai G RNA. 2004 Sep;10(9):1380-7. Epub 2004 Jul 23. PMID:15273327<ref>PMID:15273327</ref>

-	~~===Solution structure~~ of ~~an RNA stem-loop derived from~~ the ~~3' conserved region~~ of ~~eel LINE UnaL2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15273327}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1wks]] is a 1 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA].~~	+	</StructureSection>
	[[Category: Baba, S.]]		[[Category: Baba, S.]]
	[[Category: Kajikawa, M.]]		[[Category: Kajikawa, M.]]

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

2013-01-05T13:44:05Z

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

←Older revision

Revision as of 13:44, 5 January 2013

OCA at 13:44, 5 January 2013

2013-01-05T13:44:02Z

←Older revision		Revision as of 13:44, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wks.png\|left\|200px]]		[[Image:1wks.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wks", 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_1wks\| PDB=1wks \| SCENE= }}		{{STRUCTURE_1wks\| PDB=1wks \| SCENE= }}

	===Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2===		===Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15273327}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15273327 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15273327}}		{{ABSTRACT_PUBMED_15273327}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA].	+	[[1wks]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA].
-		+
-	~~==Reference==~~	+
-	Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2., Baba S, Kajikawa M, Okada N, Kawai G, RNA. 2004 Sep;10(9):1380-7. Epub 2004 Jul 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15273327 15273327]	+
	[[Category: Baba, S.]]		[[Category: Baba, S.]]
	[[Category: Kajikawa, M.]]		[[Category: Kajikawa, M.]]
Line 29:		Line 14:
	[[Category: Okada, N.]]		[[Category: Okada, N.]]
	[[Category: Line]]		[[Category: Line]]
-	[[Category: Nmr]]
	[[Category: Pentaloop]]		[[Category: Pentaloop]]
	[[Category: Retrotransposition]]		[[Category: Retrotransposition]]
	[[Category: Rna]]		[[Category: Rna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:52:43 2008''

OCA at 06:52, 29 July 2008

2008-07-29T06:52:49Z

←Older revision		Revision as of 06:52, 29 July 2008
Line 1:		Line 1:
-	[[Image:1wks.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1wks.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1wks\| PDB=1wks \| SCENE= }}		{{STRUCTURE_1wks\| PDB=1wks \| SCENE= }}

-	~~'''~~Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2~~'''~~	+	===Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2===


-	~~==Overview==~~	+	<!--
-	The ~~eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail containing a stem-loop that is critical for their retrotransposition. Presumably~~, the first step of retrotransposition is the recognition of their 3' tails by UnaL2-encoded reverse transcriptase. The solution structure of a 17-nucleotide RNA derived from the 3' tail of UnaL2 was determined by NMR. The GGAUA loop forms a specific structure in which the uridine is exposed to ~~solvent with~~ the ~~third and fifth adenosines stacked~~. ~~A sharp turn in the phosphodiester backbone occurs between the second guanosine and third adenosine~~. ~~When the uridine is mutated (but not deleted~~), ~~all mutants form~~ the loop structure, indicating that the loop structure requires an exposed fourth residue. The retrotransposition assay in HeLa cells revealed that retrotransposition requires the second guanosine, although any nucleoside functions at the fourth position, suggesting that UnaL2 reverse transcriptase specifically recognizes the 5' side of the GGANA loop.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15273327}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15273327 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15273327}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKS OCA].

	==Reference==		==Reference==
Line 29:		Line 33:
	[[Category: Retrotransposition]]		[[Category: Retrotransposition]]
	[[Category: Rna]]		[[Category: Rna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 13~~:49:03 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:52:43 2008''