4a4u - Revision history

OCA at 07:45, 18 August 2022

OCA — Thu, 18 Aug 2022 07:45:22 GMT

←Older revision		Revision as of 07:45, 18 August 2022
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	<StructureSection load='4a4u' size='340' side='right'caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='4a4u' size='340' side='right'caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4A4U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A4U 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=4a4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4u OCA], [~~http~~://pdbe.org/4a4u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4a4u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4a4u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4u 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=4a4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4u OCA], [https://pdbe.org/4a4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a4u RCSB], [https://www.ebi.ac.uk/pdbsum/4a4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fox, G]]		[[Category: Fox, G]]
	[[Category: Gao, X]]		[[Category: Gao, X]]

OCA at 09:30, 6 March 2019

OCA — Wed, 06 Mar 2019 09:30:53 GMT

←Older revision		Revision as of 09:30, 6 March 2019
Line 1:		Line 1:

	==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==		==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==
-	<StructureSection load='4a4u' size='340' side='right' caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>	+	<StructureSection load='4a4u' size='340' side='right'caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4U FirstGlance]. <br>		<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4U FirstGlance]. <br>

OCA at 08:44, 11 August 2016

OCA — Thu, 11 Aug 2016 08:44:37 GMT

←Older revision		Revision as of 08:44, 11 August 2016
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		+
	==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==		==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==
	<StructureSection load='4a4u' size='340' side='right' caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='4a4u' size='340' side='right' caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4U FirstGlance]. <br>		<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4U 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=4a4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4a4u RCSB], [http://www.ebi.ac.uk/pdbsum/4a4u 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=4a4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4u OCA], [http://pdbe.org/4a4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4a4u RCSB], [http://www.ebi.ac.uk/pdbsum/4a4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4a4u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:55, 4 January 2015

OCA — Sun, 04 Jan 2015 10:55:42 GMT

←Older revision		Revision as of 10:55, 4 January 2015
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-	[[~~Image~~:4a4u.~~jpg\|left\|200px~~]]	+	==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==
		+	<StructureSection load='4a4u' size='340' side='right' caption='[[4a4u]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4U 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=4a4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4a4u RCSB], [http://www.ebi.ac.uk/pdbsum/4a4u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structures of four small RNAs each containing a different version of the UNAC loop were determined in solution using NMR spectroscopy and restrained molecular dynamics. The UMAC tetraloops (where M is A or C) exhibited a typical GNRA fold including at least one hydrogen bond between the first U and fourth C. In contrast, UGAC and UUAC tetraloops have a different orientation of the first and fourth residues, such that they do not closely mimic the GNRA fold. Although the UMAC tetraloops are excellent structural mimics of the GNRA tetraloop backbone, sequence comparisons typically do not reveal co-variation between the two loop types. The limited covariation is attributed to differences in the location of potential hydrogen bond donors and acceptors as a result of the replacement of the terminal A of GNRA with C in the UMAC version. Thus, UMAC loops do not readily form the common GNRA tetraloop-receptor interaction. The loop at positions 863-866 in E. coli 16S ribosomal RNA appears to be a major exception. However, in this case the GNRA loop does not in fact engage in the usual base to backbone tertiary interactions. In summary, UMAC loops are not just an alternative sequence version of the GNRA loop family, but instead they expand the types of interactions, or lack thereof, that are possible. From a synthetic biology perspective their inclusion in an artificial RNA may allow the establishment of a stable loop structure while minimizing unwanted long range interactions or permitting alternative long-range interactions. (c) 2012 Wiley Periodicals, Inc. Biopolymers 97: 617-628, 2012.

-	~~<!--~~	+	UNAC tetraloops: to what extent do they mimic GNRA tetraloops?,Zhao Q, Huang HC, Nagaswamy U, Xia Y, Gao X, Fox GE Biopolymers. 2012 Aug;97(8):617-28. doi: 10.1002/bip.22049. PMID:22605553<ref>PMID:22605553</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_4a4u"~~, ~~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_4a4u\| PDB=4a4u \| SCENE= }}~~	+

-	~~===UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_22605553}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22605553 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+	[[Category: Fox, G]]
-	~~{{ABSTRACT_PUBMED_22605553}}~~	+	[[Category: Gao, X]]
-		+	[[Category: Huang, H]]
-	~~==About this Structure==~~	+	[[Category: Nagaswamy, U]]
-	~~[[4a4u]] is a 1 chain structure. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA].~~	+	[[Category: Xia, Y]]
-		+	[[Category: Zhao, Q]]
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022605553<~~/~~ref~~><~~references group="xtra"~~/>	+
-	[[Category: Fox, G.]]	+
-	[[Category: Gao, X.]]	+
-	[[Category: Huang, H.]]	+
-	[[Category: Nagaswamy, U.]]	+
-	[[Category: Xia, Y.]]	+
-	[[Category: Zhao, Q.]]	+
	[[Category: Evolution]]		[[Category: Evolution]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Umac tetraloop]]		[[Category: Umac tetraloop]]

OCA at 05:49, 30 May 2012

OCA — Wed, 30 May 2012 05:49:11 GMT

←Older revision		Revision as of 05:49, 30 May 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4a4u.jpg\|left\|200px]]

-	The ~~entry 4a4u~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4a4u", 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_4a4u\| PDB=4a4u \| SCENE= }}

-	~~Authors~~: ~~ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G.~~	+	===UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops===

-	~~Description~~: ~~UNAC Tetraloops~~: ~~To What Extent Can They Mimic GNRA Tetraloops~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22605553}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22605553 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22605553}}
		+
		+	==About this Structure==
		+	[[4a4u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4U OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022605553</ref><references group="xtra"/>
		+	[[Category: Fox, G.]]
		+	[[Category: Gao, X.]]
		+	[[Category: Huang, H.]]
		+	[[Category: Nagaswamy, U.]]
		+	[[Category: Xia, Y.]]
		+	[[Category: Zhao, Q.]]
		+	[[Category: Evolution]]
		+	[[Category: Rna]]
		+	[[Category: Umac tetraloop]]

OCA at 08:04, 2 November 2011

OCA — Wed, 02 Nov 2011 08:04:26 GMT

←Older revision		Revision as of 08:04, 2 November 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4a4u is ON HOLD ~~until sometime in the future~~	+	The entry 4a4u is ON HOLD

	Authors: ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G.		Authors: ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G.

	Description: UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops		Description: UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops

OCA: Protected "4a4u" [edit=sysop:move=sysop]

OCA — Sun, 30 Oct 2011 09:02:57 GMT

Protected "4a4u" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:02, 30 October 2011

OCA: New page: '''Unreleased structure''' The entry 4a4u is ON HOLD until sometime in the future Authors: ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G. Description: UNAC Tetraloops: T...

OCA — Sun, 30 Oct 2011 09:02:57 GMT

New page: '''Unreleased structure''' The entry 4a4u is ON HOLD until sometime in the future Authors: ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G. Description: UNAC Tetraloops: T...

New page

'''Unreleased structure'''

The entry 4a4u is ON HOLD until sometime in the future

Authors: ZHAO, Q., HUANG, H., NAGASWAMY, U., XIA, Y., GAO, X., FOX, G.

Description: UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops