4e59 - Revision history

OCA at 14:52, 14 March 2024

2024-03-14T14:52:51Z

← Older revision		Revision as of 14:52, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e59]] is a 2 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=4E59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E59 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e59]] is a 2 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=4E59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E59 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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [https://pdbe.org/4e59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [https://www.ebi.ac.uk/pdbsum/4e59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e59 ProSAT]</span></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]] 1.54Å</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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [https://pdbe.org/4e59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [https://www.ebi.ac.uk/pdbsum/4e59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e59 ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	CCG repeats are highly over-represented in exons of the human genome. Usually they are located in the 5' UTR but are also abundant in translated sequences. The CCG repeats are associated with three tri-nucleotide repeat disorders: Huntington's disease, myotonic dystrophy type 1 and chromosome X-linked mental retardation (FRAXE). In this study, we present two crystal structures containing double-stranded CCG repeats: one of an RNA in the native form, and one containing LNA nucleotides. Both duplexes form A-helices but with strands slipped in the 5' (native structure) or the 3' direction (LNA-containing structure). As a result, one of two expected C-C pairs is eliminated from the duplex. Each of the three observed C-C pairs interacts differently, forming either one weak H-bond or none. LNA nucleotides have no apparent effect on the helical parameters but the base stacking is increased compared to the native duplex and the distribution of electrostatic potential in the major groove is changed. The CCG crystal structures explain the thermodynamic fragility of CCG runs and throw light on the observation that the MBNL1 protein recognises CCG runs, as well as CUG and CAG, but not the relatively stable CGG repeats.

	Crystallographic characterization of CCG repeats.,Kiliszek A, Kierzek R, Krzyzosiak WJ, Rypniewski W Nucleic Acids Res. 2012 Sep;40(16):8155-62. doi: 10.1093/nar/gks557. Epub 2012, Jun 19. PMID:22718980<ref>PMID:22718980</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e59" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:50, 28 September 2022

2022-09-28T06:50:39Z

← Older revision		Revision as of 06:50, 28 September 2022
Line 3:		Line 3:
	<StructureSection load='4e59' size='340' side='right'caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='4e59' size='340' side='right'caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E59 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e59]] is a 2 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=4E59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E59 FirstGlance]. <br>
	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e58\|4e58]]</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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [https://pdbe.org/4e59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [https://www.ebi.ac.uk/pdbsum/4e59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e59 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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [~~http~~://pdbe.org/4e59 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e59 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e59 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kierzek, R]]		[[Category: Kierzek R]]
	[[Category: Kiliszek, A]]		[[Category: Kiliszek A]]
	[[Category: Krzyzosiak~~, W J~~]]		[[Category: Krzyzosiak WJ]]
	[[Category: Rypniewski, W]]		[[Category: Rypniewski W]]
	~~[[Category: 3' slippery duplex]]~~
	~~[[Category: Ccg repeat]]~~
	~~[[Category: Huntington's disease]]~~
	~~[[Category: Myotonic dystrophy type 1]]~~
	~~[[Category: Rna]]~~
	~~[[Category: X-linked mental retardation~~]]

OCA at 16:30, 28 August 2019

2019-08-28T16:30:54Z

← Older revision		Revision as of 16:30, 28 August 2019
Line 1:		Line 1:

	==Crystal structure of GCCGCCGC duplex==		==Crystal structure of GCCGCCGC duplex==
	<StructureSection load='4e59' size='340' side='right' caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='4e59' size='340' side='right'caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E59 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E59 FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Kierzek, R]]		[[Category: Kierzek, R]]
	[[Category: Kiliszek, A]]		[[Category: Kiliszek, A]]

OCA at 02:51, 11 December 2016

2016-12-11T02:51:28Z

← Older revision		Revision as of 02:51, 11 December 2016
Line 1:		Line 1:

	==Crystal structure of GCCGCCGC duplex==		==Crystal structure of GCCGCCGC duplex==
	<StructureSection load='4e59' size='340' side='right' caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='4e59' size='340' side='right' caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E59 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E59 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e58\|4e58]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e58\|4e58]]</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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [http://www.ebi.ac.uk/pdbsum/4e59 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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [http://pdbe.org/4e59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [http://www.ebi.ac.uk/pdbsum/4e59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e59 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		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 4e59" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:55, 9 December 2014

2014-12-09T16:55:50Z

← Older revision		Revision as of 16:55, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e59~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Crystal structure of GCCGCCGC duplex==
			<StructureSection load='4e59' size='340' side='right' caption='[[4e59]], [[Resolution\|resolution]] 1.54Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E59 FirstGlance]. <br>
			</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e58\|4e58]]</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=4e59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e59 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e59 RCSB], [http://www.ebi.ac.uk/pdbsum/4e59 PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			CCG repeats are highly over-represented in exons of the human genome. Usually they are located in the 5' UTR but are also abundant in translated sequences. The CCG repeats are associated with three tri-nucleotide repeat disorders: Huntington's disease, myotonic dystrophy type 1 and chromosome X-linked mental retardation (FRAXE). In this study, we present two crystal structures containing double-stranded CCG repeats: one of an RNA in the native form, and one containing LNA nucleotides. Both duplexes form A-helices but with strands slipped in the 5' (native structure) or the 3' direction (LNA-containing structure). As a result, one of two expected C-C pairs is eliminated from the duplex. Each of the three observed C-C pairs interacts differently, forming either one weak H-bond or none. LNA nucleotides have no apparent effect on the helical parameters but the base stacking is increased compared to the native duplex and the distribution of electrostatic potential in the major groove is changed. The CCG crystal structures explain the thermodynamic fragility of CCG runs and throw light on the observation that the MBNL1 protein recognises CCG runs, as well as CUG and CAG, but not the relatively stable CGG repeats.

	~~{{STRUCTURE_4e59\| PDB=4e59 \| SCENE= }}~~		Crystallographic characterization of CCG repeats.,Kiliszek A, Kierzek R, Krzyzosiak WJ, Rypniewski W Nucleic Acids Res. 2012 Sep;40(16):8155-62. doi: 10.1093/nar/gks557. Epub 2012, Jun 19. PMID:22718980<ref>PMID:22718980</ref>

	~~===Crystal structure~~ of ~~GCCGCCGC duplex===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22718980}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA].~~		</StructureSection>
	[[Category: Kierzek, R.]]		[[Category: Kierzek, R]]
	[[Category: Kiliszek, A.]]		[[Category: Kiliszek, A]]
	[[Category: Krzyzosiak, W J.]]		[[Category: Krzyzosiak, W J]]
	[[Category: Rypniewski, W.]]		[[Category: Rypniewski, W]]
	[[Category: 3' slippery duplex]]		[[Category: 3' slippery duplex]]
	[[Category: Ccg repeat]]		[[Category: Ccg repeat]]

OCA at 21:13, 12 December 2012

2012-12-12T21:13:57Z

← Older revision		Revision as of 21:13, 12 December 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e59.jpg\|left\|200px]]

	~~The entry~~ 4e59 ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e59\| PDB=4e59 \| SCENE= }}

	~~Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W.~~		===Crystal structure of GCCGCCGC duplex===

	~~Description~~: ~~Crystal structure of GCCGCCGC~~ duplex		{{ABSTRACT_PUBMED_22718980}}

			==About this Structure==
			[[4e59]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E59 OCA].
			[[Category: Kierzek, R.]]
			[[Category: Kiliszek, A.]]
			[[Category: Krzyzosiak, W J.]]
			[[Category: Rypniewski, W.]]
			[[Category: 3' slippery duplex]]
			[[Category: Ccg repeat]]
			[[Category: Huntington's disease]]
			[[Category: Myotonic dystrophy type 1]]
			[[Category: Rna]]
			[[Category: X-linked mental retardation]]

OCA at 07:29, 18 April 2012

2012-04-18T07:29:03Z

← Older revision		Revision as of 07:29, 18 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e59 is ON HOLD		The entry 4e59 is ON HOLD until Paper Publication

	Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W.		Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W.

	Description: Crystal structure of GCCGCCGC duplex		Description: Crystal structure of GCCGCCGC duplex

OCA: Protected "4e59" [edit=sysop:move=sysop]

2012-03-21T07:17:43Z

Protected "4e59" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:17, 21 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e59 is ON HOLD Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W. Description: Crystal structure of GCCGCCGC duplex

2012-03-21T07:17:41Z

New page: '''Unreleased structure''' The entry 4e59 is ON HOLD Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W. Description: Crystal structure of GCCGCCGC duplex

New page

'''Unreleased structure'''

The entry 4e59 is ON HOLD

Authors: Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., Rypniewski, W.

Description: Crystal structure of GCCGCCGC duplex