2d1b - Revision history

OCA at 16:34, 13 December 2023

2023-12-13T16:34:03Z

←Older revision		Revision as of 16:34, 13 December 2023
Line 1:		Line 1:

	==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==		==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==
-	<StructureSection load='2d1b' size='340' side='right'caption='[[2d1b~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='2d1b' size='340' side='right'caption='[[2d1b]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</div~~></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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [https://pdbe.org/2d1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [https://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b 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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [https://pdbe.org/2d1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [https://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baba, S]]	+	[[Category: Baba S]]
-	[[Category: Kawai, G]]	+	[[Category: Kawai G]]
-	[[Category: Koyanagi, Y]]	+	[[Category: Koyanagi Y]]
-	[[Category: Noguchi, S]]	+	[[Category: Noguchi S]]
-	[[Category: Takahashi, K]]	+	[[Category: Takahashi K]]
-	[[Category: Takaku, H]]	+	[[Category: Takaku H]]
-	[[Category: Yamamoto, N]]	+	[[Category: Yamamoto N]]
-	~~[[Category: Di]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 10:25, 8 December 2021

2021-12-08T10:25:26Z

←Older revision		Revision as of 10:25, 8 December 2021
Line 3:		Line 3:
	<StructureSection load='2d1b' size='340' side='right'caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2d1b' size='340' side='right'caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D1B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</div></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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [~~http~~://pdbe.org/2d1b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b 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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [https://pdbe.org/2d1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [https://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:47, 4 March 2020

2020-03-04T07:47:21Z

←Older revision		Revision as of 07:47, 4 March 2020
Line 1:		Line 1:

	==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==		==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==
-	<StructureSection load='2d1b' size='340' side='right' caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='2d1b' size='340' side='right'caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
	[[Category: Kawai, G]]		[[Category: Kawai, G]]

OCA at 06:34, 30 May 2018

2018-05-30T06:34:16Z

←Older revision		Revision as of 06:34, 30 May 2018
Line 1:		Line 1:
		+
	==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==		==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==
	<StructureSection load='2d1b' size='340' side='right' caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2d1b' size='340' side='right' caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [http://pdbe.org/2d1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [http://www.ebi.ac.uk/pdbsum/2d1b 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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [http://pdbe.org/2d1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [http://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:08, 11 September 2015

2015-09-11T16:08:22Z

←Older revision		Revision as of 16:08, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [http://www.ebi.ac.uk/pdbsum/2d1b 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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [http://pdbe.org/2d1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [http://www.ebi.ac.uk/pdbsum/2d1b PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 2d1b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:09, 15 January 2015

2015-01-15T18:09:14Z

←Older revision		Revision as of 18:09, 15 January 2015
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baba, S.]]	+	[[Category: Baba, S]]
-	[[Category: Kawai, G.]]	+	[[Category: Kawai, G]]
-	[[Category: Koyanagi, Y.]]	+	[[Category: Koyanagi, Y]]
-	[[Category: Noguchi, S.]]	+	[[Category: Noguchi, S]]
-	[[Category: Takahashi, K.]]	+	[[Category: Takahashi, K]]
-	[[Category: Takaku, H.]]	+	[[Category: Takaku, H]]
-	[[Category: Yamamoto, N.]]	+	[[Category: Yamamoto, N]]
	[[Category: Di]]		[[Category: Di]]
	[[Category: Hiv-1]]		[[Category: Hiv-1]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 08:15, 8 October 2014

2014-10-08T08:15:51Z

←Older revision		Revision as of 08:15, 8 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2d1b.~~png~~\|~~left~~\|~~200px~~]]	+	==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer==
		+	<StructureSection load='2d1b' size='340' side='right' caption='[[2d1b]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1B FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d17\|2d17]], [[2d18\|2d18]], [[2d19\|2d19]], [[2d1a\|2d1a]]</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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [http://www.ebi.ac.uk/pdbsum/2d1b PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dimer formation of HIV-1 genomic RNA through its dimerization initiation site (DIS) is crucial to maintaining infectivity. Two types of dimers, the initially generated kissing-loop dimer and the subsequent product of the extended-duplex dimer, are formed in the stem-bulge-stem region with a loop including a self-complementary sequence. NMR chemical shift analysis of a 39mer RNA corresponding to DIS, DIS39, in the kissing-loop and extended-duplex dimers revealed that the three dimensional structures of the stem-bulge-stem region are extremely similar between the two types of dimers. Therefore, we designed two shorter RNA molecules, loop25 and bulge34, corresponding to the loop-stem region and the stem-bulge-stem region of DIS39, respectively. Based upon the chemical shift analysis, the conformation of the loop region of loop25 is identical to that of DIS39 for each of the two types of dimers. The conformation of bulge34 was also found to be the same as that of the corresponding region of DIS39. Thus, we determined the solution structures of loop25 in each of the two types of dimers as well as that of bulge34. Finally, the solution structures of DIS39 in the kissing-loop and extended-duplex dimers were determined by combining the parts of the structures. The solution structures of the two types of dimers were similar to each other in general with a difference found only in the A16 residue. The elucidation of the structures of DIS39 is important to understanding the molecular mechanism of the conformational dynamics of viral RNA molecules.

-	~~{{STRUCTURE_2d1b\| PDB=2d1b \| SCENE= }}~~	+	Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.,Baba S, Takahashi K, Noguchi S, Takaku H, Koyanagi Y, Yamamoto N, Kawai G J Biochem. 2005 Nov;138(5):583-92. PMID:16272570<ref>PMID:16272570</ref>

-	~~===Solution RNA structure model~~ of the ~~HIV-1 dimerization initiation site in the kissing-loop dimer===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16272570}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2d1b]] is a 2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2D1B OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016272570<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Baba, S.]]		[[Category: Baba, S.]]
	[[Category: Kawai, G.]]		[[Category: Kawai, G.]]

OCA: Protected "2d1b" [edit=sysop:move=sysop]

2013-01-06T11:56:57Z

Protected "2d1b" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:56, 6 January 2013

OCA at 11:56, 6 January 2013

2013-01-06T11:56:53Z

←Older revision		Revision as of 11:56, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2d1b.png\|left\|200px]]		[[Image:2d1b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2d1b", 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_2d1b\| PDB=2d1b \| SCENE= }}		{{STRUCTURE_2d1b\| PDB=2d1b \| SCENE= }}

	===Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer===		===Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16272570}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16272570 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16272570}}		{{ABSTRACT_PUBMED_16272570}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA].	+	[[2d1b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA].

	==Reference==		==Reference==
-	Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers., Baba S, Takahashi K, Noguchi S, Takaku H, Koyanagi Y, Yamamoto N, Kawai G, J Biochem. 2005 Nov;138(5):583-92. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16272570 16272570]~~	+	<ref group="xtra">PMID:016272570</ref><references group="xtra"/>
	[[Category: Baba, S.]]		[[Category: Baba, S.]]
	[[Category: Kawai, G.]]		[[Category: Kawai, G.]]
Line 33:		Line 21:
	[[Category: Di]]		[[Category: Di]]
	[[Category: Hiv-1]]		[[Category: Hiv-1]]
-	[[Category: Nmr]]
	[[Category: Rna]]		[[Category: Rna]]
-	[[Category: Structure]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:40:19 2008''

OCA at 06:40, 29 July 2008

2008-07-29T06:40:25Z

←Older revision		Revision as of 06:40, 29 July 2008
Line 1:		Line 1:
-	[[Image:2d1b.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2d1b.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2d1b\| PDB=2d1b \| SCENE= }}		{{STRUCTURE_2d1b\| PDB=2d1b \| SCENE= }}

-	~~'''~~Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer~~'''~~	+	===Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer===


-	~~==Overview==~~	+	<!--
-	~~Dimer formation of HIV~~-~~1 genomic RNA through its dimerization initiation site (DIS) is crucial to maintaining infectivity. Two types of dimers, the initially generated kissing~~-~~loop dimer and the subsequent product of the extended-duplex dimer~~, ~~are formed in the stem-bulge-stem region with a loop including a self-complementary sequence. NMR chemical shift analysis of a 39mer RNA corresponding to DIS~~, ~~DIS39, in~~ the kissing-loop and extended-duplex dimers revealed that the three dimensional structures of the stem-bulge-stem region are extremely similar between the two types of dimers. Therefore, we designed two shorter RNA molecules, loop25 and bulge34, corresponding to the ~~loop-stem region and the stem-bulge-stem region of DIS39, respectively~~. ~~Based upon the chemical shift analysis~~, ~~the conformation of the loop region of loop25~~ is ~~identical to that of DIS39 for each of~~ the ~~two types of dimers~~. The conformation of bulge34 was also found to be the same as that of the corresponding region of DIS39. Thus, we determined the solution structures of loop25 in each of the two types of dimers as well as that of bulge34. Finally, the solution structures of DIS39 in the kissing-~~loop and extended~~-duplex dimers were determined by combining the parts of the structures. The solution structures of the two types of dimers were similar to each other in general with a difference found only in the A16 residue. The elucidation of the structures of DIS39 is important to understanding the molecular mechanism of the conformational dynamics of viral RNA molecules.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16272570}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16272570 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16272570}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA].

	==Reference==		==Reference==
Line 32:		Line 36:
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Structure]]		[[Category: Structure]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 23~~:30:29 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:40:19 2008''