1t4x - Revision history

OCA at 09:25, 6 December 2023

OCA — Wed, 06 Dec 2023 09:25:36 GMT

←Older revision		Revision as of 09:25, 6 December 2023
Line 1:		Line 1:

	==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==		==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==
-	<StructureSection load='1t4x' size='340' side='right'caption='[[1t4x~~]], [[NMR_Ensembles_of_Models \| 12 NMR models~~]]' scene=''>	+	<StructureSection load='1t4x' size='340' side='right'caption='[[1t4x]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T4X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T4X 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [https://pdbe.org/1t4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [https://www.ebi.ac.uk/pdbsum/1t4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4x 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [https://pdbe.org/1t4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [https://www.ebi.ac.uk/pdbsum/1t4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adamiak~~, R W~~]]	+	[[Category: Adamiak RW]]
-	[[Category: Milecki, J]]	+	[[Category: Milecki J]]
-	[[Category: Popenda, M]]	+	[[Category: Popenda M]]
-	~~[[Category: Left-handed rna duplex]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Z-rna~~]]	+

OCA at 07:41, 22 September 2021

OCA — Wed, 22 Sep 2021 07:41:23 GMT

←Older revision		Revision as of 07:41, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1t4x' size='340' side='right'caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>		<StructureSection load='1t4x' size='340' side='right'caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T4X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T4X 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [~~http~~://pdbe.org/1t4x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t4x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4x 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [https://pdbe.org/1t4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [https://www.ebi.ac.uk/pdbsum/1t4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:12, 18 December 2019

OCA — Wed, 18 Dec 2019 14:12:08 GMT

←Older revision		Revision as of 14:12, 18 December 2019
Line 1:		Line 1:

	==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==		==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==
-	<StructureSection load='1t4x' size='340' side='right' caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>	+	<StructureSection load='1t4x' size='340' side='right'caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Adamiak, R W]]		[[Category: Adamiak, R W]]
	[[Category: Milecki, J]]		[[Category: Milecki, J]]

OCA at 07:52, 14 March 2018

OCA — Wed, 14 Mar 2018 07:52:24 GMT

←Older revision		Revision as of 07:52, 14 March 2018
Line 1:		Line 1:
		+
	==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==		==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==
	<StructureSection load='1t4x' size='340' side='right' caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>		<StructureSection load='1t4x' size='340' side='right' caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [http://pdbe.org/1t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [http://www.ebi.ac.uk/pdbsum/1t4x 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [http://pdbe.org/1t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [http://www.ebi.ac.uk/pdbsum/1t4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:50, 10 September 2015

OCA — Thu, 10 Sep 2015 15:50:39 GMT

←Older revision		Revision as of 15:50, 10 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [http://www.ebi.ac.uk/pdbsum/1t4x 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [http://pdbe.org/1t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [http://www.ebi.ac.uk/pdbsum/1t4x 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 1t4x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:15, 15 January 2015

OCA — Thu, 15 Jan 2015 18:15:57 GMT

←Older revision		Revision as of 18:15, 15 January 2015
Line 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Adamiak, R W.]]	+	[[Category: Adamiak, R W]]
-	[[Category: Milecki, J.]]	+	[[Category: Milecki, J]]
-	[[Category: Popenda, M.]]	+	[[Category: Popenda, M]]
	[[Category: Left-handed rna duplex]]		[[Category: Left-handed rna duplex]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Z-rna]]		[[Category: Z-rna]]

OCA at 08:19, 8 October 2014

OCA — Wed, 08 Oct 2014 08:19:33 GMT

←Older revision		Revision as of 08:19, 8 October 2014
Line 1:		Line 1:
-	[[~~Image~~:1t4x.~~png\|left\|200px~~]]	+	==The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt==
		+	<StructureSection load='1t4x' size='340' side='right' caption='[[1t4x]], [[NMR_Ensembles_of_Models \| 12 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4X 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=1t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4x RCSB], [http://www.ebi.ac.uk/pdbsum/1t4x PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'/H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4-7 degrees), whereas GpC steps have large negative values (-61 degrees). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2'-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.

-	~~{{STRUCTURE_1t4x\| PDB=1t4x \| SCENE= }}~~	+	High salt solution structure of a left-handed RNA double helix.,Popenda M, Milecki J, Adamiak RW Nucleic Acids Res. 2004 Aug 3;32(13):4044-54. Print 2004. PMID:15292450<ref>PMID:15292450</ref>

-	~~===The first left-handed RNA structure~~ of ~~(CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15292450}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1t4x]] is a 2 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA].~~	+	</StructureSection>
	[[Category: Adamiak, R W.]]		[[Category: Adamiak, R W.]]
	[[Category: Milecki, J.]]		[[Category: Milecki, J.]]

OCA: Protected "1t4x" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:37:06 GMT

Protected "1t4x" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:37, 5 January 2013

OCA at 13:37, 5 January 2013

OCA — Sat, 05 Jan 2013 13:37:03 GMT

←Older revision		Revision as of 13:37, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t4x.png\|left\|200px]]		[[Image:1t4x.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t4x", 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_1t4x\| PDB=1t4x \| SCENE= }}		{{STRUCTURE_1t4x\| PDB=1t4x \| SCENE= }}

	===The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt===		===The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15292450}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15292450 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15292450}}		{{ABSTRACT_PUBMED_15292450}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA].	+	[[1t4x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA].
-		+
-	~~==Reference==~~	+
-	High salt solution structure of a left-handed RNA double helix., Popenda M, Milecki J, Adamiak RW, Nucleic Acids Res. 2004 Aug 3;32(13):4044-54. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15292450 15292450]	+
	[[Category: Adamiak, R W.]]		[[Category: Adamiak, R W.]]
	[[Category: Milecki, J.]]		[[Category: Milecki, J.]]
	[[Category: Popenda, M.]]		[[Category: Popenda, M.]]
	[[Category: Left-handed rna duplex]]		[[Category: Left-handed rna duplex]]
		+	[[Category: Rna]]
	[[Category: Z-rna]]		[[Category: Z-rna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:17:41 2008''

OCA at 04:17, 28 July 2008

OCA — Mon, 28 Jul 2008 04:17:48 GMT

←Older revision		Revision as of 04:17, 28 July 2008
Line 1:		Line 1:
-	[[Image:1t4x.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1t4x.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1t4x\| PDB=1t4x \| SCENE= }}		{{STRUCTURE_1t4x\| PDB=1t4x \| SCENE= }}

-	~~'''~~The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt~~'''~~	+	===The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt===


-	~~==Overview==~~	+	<!--
-	~~Right~~-~~handed RNA duplexes of (CG)n sequence undergo salt~~-~~induced helicity reversal~~, ~~forming left-handed RNA double helices (Z-RNA). In contrast~~ to the ~~thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix~~ (~~CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined~~ at ~~such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'~~/~~H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices~~. ~~Z-RNA structure shows several conformational features significantly different from Z-DNA~~. ~~Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4-7 degrees~~), ~~whereas GpC steps have large negative values (-61 degrees). In~~ the ~~full-turn model of Z-RNA (12~~.~~4 bp per turn), base pairs are much closer to the helix axis than in Z~~-~~DNA, thus both the very deep, narrow minor groove with buried cytidine 2'~~-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15292450}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15292450 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15292450}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4X OCA].

	==Reference==		==Reference==
Line 25:		Line 29:
	[[Category: Left-handed rna duplex]]		[[Category: Left-handed rna duplex]]
	[[Category: Z-rna]]		[[Category: Z-rna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 09~~:32:05 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:17:41 2008''