1y99 - Revision history

OCA at 07:14, 9 August 2023

2023-08-09T07:14:10Z

←Older revision		Revision as of 07:14, 9 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [https://pdbe.org/1y99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [https://www.ebi.ac.uk/pdbsum/1y99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y99 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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [https://pdbe.org/1y99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [https://www.ebi.ac.uk/pdbsum/1y99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y99 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dumas, P]]	+	[[Category: Dumas P]]
-	[[Category: Ehresmann, B]]	+	[[Category: Ehresmann B]]
-	[[Category: Ehresmann, C]]	+	[[Category: Ehresmann C]]
-	[[Category: Ennifar, E]]	+	[[Category: Ennifar E]]
-	[[Category: Marquet, R]]	+	[[Category: Marquet R]]
-	[[Category: Walter, P]]	+	[[Category: Walter P]]
-	[[Category: Yusupov, M]]	+	[[Category: Yusupov M]]
-	~~[[Category: Bulge]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 16:24, 3 November 2021

2021-11-03T16:24:59Z

←Older revision		Revision as of 16:24, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1y99' size='340' side='right'caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1y99' size='340' side='right'caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [~~http~~://pdbe.org/1y99 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y99 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y99 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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [https://pdbe.org/1y99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [https://www.ebi.ac.uk/pdbsum/1y99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y99 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:14, 29 January 2020

2020-01-29T17:14:53Z

←Older revision		Revision as of 17:14, 29 January 2020
Line 1:		Line 1:

	==HIV-1 subtype A DIS RNA duplex==		==HIV-1 subtype A DIS RNA duplex==
-	<StructureSection load='1y99' size='340' side='right' caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1y99' size='340' side='right'caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dumas, P]]		[[Category: Dumas, P]]
	[[Category: Ehresmann, B]]		[[Category: Ehresmann, B]]

OCA at 06:57, 25 April 2018

2018-04-25T06:57:45Z

←Older revision		Revision as of 06:57, 25 April 2018
Line 1:		Line 1:
		+
	==HIV-1 subtype A DIS RNA duplex==		==HIV-1 subtype A DIS RNA duplex==
	<StructureSection load='1y99' size='340' side='right' caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1y99' size='340' side='right' caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://pdbe.org/1y99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://pdbe.org/1y99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y99 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:00, 11 September 2015

2015-09-11T02:00:14Z

←Older revision		Revision as of 02:00, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://pdbe.org/1y99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 1y99" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:54, 22 December 2014

2014-12-22T05:54:01Z

←Older revision		Revision as of 05:54, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 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=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dumas, P.]]	+	[[Category: Dumas, P]]
-	[[Category: Ehresmann, B.]]	+	[[Category: Ehresmann, B]]
-	[[Category: Ehresmann, C.]]	+	[[Category: Ehresmann, C]]
-	[[Category: Ennifar, E.]]	+	[[Category: Ennifar, E]]
-	[[Category: Marquet, R.]]	+	[[Category: Marquet, R]]
-	[[Category: Walter, P.]]	+	[[Category: Walter, P]]
-	[[Category: Yusupov, M.]]	+	[[Category: Yusupov, M]]
	[[Category: Bulge]]		[[Category: Bulge]]
	[[Category: Hiv-1]]		[[Category: Hiv-1]]
	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 07:07, 9 June 2014

2014-06-09T07:07:26Z

←Older revision		Revision as of 07:07, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1y99.~~png~~\|~~left~~\|~~200px~~]]	+	==HIV-1 subtype A DIS RNA duplex==
		+	<StructureSection load='1y99' size='340' side='right' caption='[[1y99]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y99 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[462d\|462d]], [[1jjn\|1jjn]], [[1k9w\|1k9w]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y99 RCSB], [http://www.ebi.ac.uk/pdbsum/1y99 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.

-	~~{{STRUCTURE_1y99\| PDB=1y99 \| SCENE= }}~~	+	The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.,Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P Structure. 1999 Nov 15;7(11):1439-49. PMID:10574792<ref>PMID:10574792</ref>

-	~~===HIV-1 subtype A DIS RNA duplex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10574792}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y99]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1Y99 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010574792<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Dumas, P.]]		[[Category: Dumas, P.]]
	[[Category: Ehresmann, B.]]		[[Category: Ehresmann, B.]]

OCA: Protected "1y99" [edit=sysop:move=sysop]

2012-08-14T16:22:11Z

Protected "1y99" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:22, 14 August 2012

OCA at 16:22, 14 August 2012

2012-08-14T16:22:09Z

←Older revision		Revision as of 16:22, 14 August 2012
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-	{{Seed}}
	[[Image:1y99.png\|left\|200px]]		[[Image:1y99.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1y99\| PDB=1y99 \| SCENE= }}		{{STRUCTURE_1y99\| PDB=1y99 \| SCENE= }}

	===HIV-1 subtype A DIS RNA duplex===		===HIV-1 subtype A DIS RNA duplex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10574792}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_10574792}}		{{ABSTRACT_PUBMED_10574792}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA].	+	[[1y99]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y99 OCA].

	==Reference==		==Reference==
-	The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges., Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P, Structure. 1999 Nov 15;7(11):1439-49. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~10574792 10574792]~~	+	<ref group="xtra">PMID:010574792</ref><references group="xtra"/>
	[[Category: Dumas, P.]]		[[Category: Dumas, P.]]
	[[Category: Ehresmann, B.]]		[[Category: Ehresmann, B.]]
Line 35:		Line 23:
	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Rna]]		[[Category: Rna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:07:29 2008''

OCA at 14:07, 28 July 2008

2008-07-28T14:07:33Z

←Older revision		Revision as of 14:07, 28 July 2008
Line 1:		Line 1:
-	[[Image:1y99.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1y99.png\|left\|200px]]

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	{{STRUCTURE_1y99\| PDB=1y99 \| SCENE= }}		{{STRUCTURE_1y99\| PDB=1y99 \| SCENE= }}

-	~~'''~~HIV-1 subtype A DIS RNA duplex~~'''~~	+	===HIV-1 subtype A DIS RNA duplex===


-	~~==Overview==~~	+	<!--
-	~~BACKGROUND: An important step in retroviral replication is dimerization of~~ the ~~genomic RNA prior~~ to ~~encapsidation. Dimerization is initiated by~~ the ~~formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein~~ (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: ~~The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2~~.~~3 A resolution in two different space groups~~. ~~It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches~~, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the ~~3' phosphate of each bulge across an extremely narrowed deep major groove~~. ~~CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing~~-~~loop complex. They show the ability of this self~~-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.	+	The line below this paragraph, {{ABSTRACT_PUBMED_10574792}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10574792 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10574792}}

	==About this Structure==		==About this Structure==
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	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Rna]]		[[Category: Rna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 16~~:02:04 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:07:29 2008''