4xw1 - Revision history

OCA at 10:51, 10 January 2024

OCA — Wed, 10 Jan 2024 10:51:10 GMT

←Older revision		Revision as of 10:51, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</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]] 2.302Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [https://pdbe.org/4xw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [https://www.ebi.ac.uk/pdbsum/4xw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw1 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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [https://pdbe.org/4xw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [https://www.ebi.ac.uk/pdbsum/4xw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw1 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:54, 26 April 2023

OCA — Wed, 26 Apr 2023 17:54:40 GMT

←Older revision		Revision as of 17:54, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xw1' size='340' side='right'caption='[[4xw1]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xw1' size='340' side='right'caption='[[4xw1]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xw0\|4xw0]]~~</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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [https://pdbe.org/4xw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [https://www.ebi.ac.uk/pdbsum/4xw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw1 ProSAT]</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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [~~http~~://pdbe.org/4xw1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xw1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw1 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banaszak, K]]	+	[[Category: Banaszak K]]
-	[[Category: Kiliszek, A]]	+	[[Category: Kiliszek A]]
-	[[Category: Rypniewski, W]]	+	[[Category: Rypniewski W]]
-	~~[[Category: 3' overhanging nucleotide]]~~	+
-	~~[[Category: Ccug repeat]]~~	+
-	~~[[Category: Lna residue]]~~	+
-	~~[[Category: Myotonic dystrophy type 2]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna duplex]]~~	+
-	~~[[Category: Tautomery~~]]	+

OCA at 00:07, 6 June 2019

OCA — Thu, 06 Jun 2019 00:07:19 GMT

←Older revision		Revision as of 00:07, 6 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of (GCCU(G-LNA)CCUG)2 duplex==		==Crystal structure of (GCCU(G-LNA)CCUG)2 duplex==
-	<StructureSection load='4xw1' size='340' side='right' caption='[[4xw1]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4xw1' size='340' side='right'caption='[[4xw1]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xw0\|4xw0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xw0\|4xw0]]</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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [http://pdbe.org/4xw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4xw1 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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [http://pdbe.org/4xw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4xw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Banaszak, K]]		[[Category: Banaszak, K]]
	[[Category: Kiliszek, A]]		[[Category: Kiliszek, A]]

OCA at 20:14, 13 January 2016

OCA — Wed, 13 Jan 2016 20:14:57 GMT

←Older revision		Revision as of 20:14, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of (GCCU(G-LNA)CCUG)2 duplex==
		+	<StructureSection load='4xw1' size='340' side='right' caption='[[4xw1]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XW1 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xw0\|4xw0]]</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=4xw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw1 OCA], [http://pdbe.org/4xw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4xw1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA transcripts that include expanded CCUG repeats are associated with myotonic dystrophy type 2. Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing. The overhanging ends of the duplexes interact forming U-U pairs, which also show tautomerism. Duplexes consisting of CCUG repeats are thermodynamically less stable than the trinucleotide repeats involved in the TRED genetic disorders, but introducing LNA residues increases their stability and raises the melting temperature of the studied oligomers by approximately 10 degrees C, allowing detailed crystallographic studies. Quantum mechanical calculations were performed to test the possibility of the tautomeric transitions or protonation within the noncanonical pairs. The results indicate that tautomeric or ionic shifts of nucleobases can manifest themselves in biological systems, supplementing the canonical "rules of engagement."

-	~~The entry 4xw1 is ON HOLD until Paper Publication~~	+	Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.,Rypniewski W, Banaszak K, Kulinski T, Kiliszek A RNA. 2016 Jan;22(1):22-31. doi: 10.1261/rna.052399.115. Epub 2015 Nov 5. PMID:26543073<ref>PMID:26543073</ref>

-	~~Authors: Kiliszek~~, A.~~, Banaszak, K~~.~~, Rypniewski, W~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of (GCCU(G-LNA)CCUG)2 duplex~~	+	<div class="pdbe-citations 4xw1" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Banaszak, K]]		[[Category: Banaszak, K]]
		+	[[Category: Kiliszek, A]]
	[[Category: Rypniewski, W]]		[[Category: Rypniewski, W]]
-	[[Category: ~~Kiliszek, A~~]]	+	[[Category: 3' overhanging nucleotide]]
		+	[[Category: Ccug repeat]]
		+	[[Category: Lna residue]]
		+	[[Category: Myotonic dystrophy type 2]]
		+	[[Category: Rna]]
		+	[[Category: Rna duplex]]
		+	[[Category: Tautomery]]

OCA at 23:20, 30 November 2015

OCA — Mon, 30 Nov 2015 23:20:55 GMT

←Older revision		Revision as of 23:20, 30 November 2015
Line 7:		Line 7:
	Description: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex		Description: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kiliszek, A]]
	[[Category: Banaszak, K]]		[[Category: Banaszak, K]]
	[[Category: Rypniewski, W]]		[[Category: Rypniewski, W]]
		+	[[Category: Kiliszek, A]]

OCA at 11:44, 18 February 2015

OCA — Wed, 18 Feb 2015 11:44:10 GMT

←Older revision		Revision as of 11:44, 18 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xw1 is ON HOLD	+	The entry 4xw1 is ON HOLD until Paper Publication

	Authors: Kiliszek, A., Banaszak, K., Rypniewski, W.		Authors: Kiliszek, A., Banaszak, K., Rypniewski, W.

OCA: Protected "4xw1" [edit=sysop:move=sysop]

OCA — Sat, 07 Feb 2015 14:53:42 GMT

Protected "4xw1" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:53, 7 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xw1 is ON HOLD Authors: Kiliszek, A., Banaszak, K., Rypniewski, W. Description: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex [[Category: Unrelea...

OCA — Sat, 07 Feb 2015 14:53:41 GMT

New page: '''Unreleased structure''' The entry 4xw1 is ON HOLD Authors: Kiliszek, A., Banaszak, K., Rypniewski, W. Description: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 4xw1 is ON HOLD

Authors: Kiliszek, A., Banaszak, K., Rypniewski, W.

Description: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex
[[Category: Unreleased Structures]]
[[Category: Kiliszek, A]]
[[Category: Banaszak, K]]
[[Category: Rypniewski, W]]