4qkk - Revision history

OCA at 08:59, 20 March 2024

OCA — Wed, 20 Mar 2024 08:59:03 GMT

←Older revision		Revision as of 08:59, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QKK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QKK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [https://pdbe.org/4qkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [https://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk 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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [https://pdbe.org/4qkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [https://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-A-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.
-
-	5-Formylcytosine alters the structure of the DNA double helix.,Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S Nat Struct Mol Biol. 2015 Jan;22(1):44-49. doi: 10.1038/nsmb.2936. Epub 2014 Dec , 15. PMID:25504322<ref>PMID:25504322</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4qkk" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:33, 15 February 2023

OCA — Wed, 15 Feb 2023 11:33:38 GMT

←Older revision		Revision as of 11:33, 15 February 2023
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	<StructureSection load='4qkk' size='340' side='right'caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4qkk' size='340' side='right'caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QKK FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene></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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [~~http~~://pdbe.org/4qkk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk 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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [https://pdbe.org/4qkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [https://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Balasubramanian, S]]	+	[[Category: Synthetic construct]]
-	[[Category: Chirgadze~~, D Y~~]]	+	[[Category: Balasubramanian S]]
-	[[Category: Luisi~~, B F~~]]	+	[[Category: Chirgadze DY]]
-	[[Category: Murat, P]]	+	[[Category: Luisi BF]]
-	[[Category: Raiber, E A]]	+	[[Category: Murat P]]
-	~~[[Category: Dna]]~~	+	[[Category: Raiber E-A]]
-	~~[[Category: Epigenetic ten-eleven]]~~	+
-	~~[[Category: Formylcytosine]]~~	+
-	~~[[Category: Oligonucleotide]]~~	+
-	~~[[Category: Thymine dna glycosylase]]~~	+
-	~~[[Category: Translocation protein~~]]	+

OCA at 10:16, 25 December 2019

OCA — Wed, 25 Dec 2019 10:16:43 GMT

←Older revision		Revision as of 10:16, 25 December 2019
Line 7:		Line 7:
	<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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [http://pdbe.org/4qkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [http://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk 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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [http://pdbe.org/4qkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [http://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-A-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.
		+
		+	5-Formylcytosine alters the structure of the DNA double helix.,Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S Nat Struct Mol Biol. 2015 Jan;22(1):44-49. doi: 10.1038/nsmb.2936. Epub 2014 Dec , 15. PMID:25504322<ref>PMID:25504322</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4qkk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:29, 24 April 2019

OCA — Wed, 24 Apr 2019 09:29:40 GMT

←Older revision		Revision as of 09:29, 24 April 2019
Line 1:		Line 1:

	==Crystal structure of an oligonucleotide containing 5-formylcytosine==		==Crystal structure of an oligonucleotide containing 5-formylcytosine==
-	<StructureSection load='4qkk' size='340' side='right' caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='4qkk' size='340' side='right'caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QKK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QKK FirstGlance]. <br>
Line 9:		Line 9:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Balasubramanian, S]]		[[Category: Balasubramanian, S]]
	[[Category: Chirgadze, D Y]]		[[Category: Chirgadze, D Y]]

OCA at 17:10, 4 January 2017

OCA — Wed, 04 Jan 2017 17:10:00 GMT

←Older revision		Revision as of 17:10, 4 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of an oligonucleotide containing 5-formylcytosine==		==Crystal structure of an oligonucleotide containing 5-formylcytosine==
	<StructureSection load='4qkk' size='340' side='right' caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4qkk' size='340' side='right' caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QKK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QKK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</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=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene></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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [http://www.ebi.ac.uk/pdbsum/4qkk 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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [http://pdbe.org/4qkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [http://www.ebi.ac.uk/pdbsum/4qkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qkk ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 16:23, 10 December 2014

OCA — Wed, 10 Dec 2014 16:23:29 GMT

←Older revision		Revision as of 16:23, 10 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of an oligonucleotide containing 5-formylcytosine==
-		+	<StructureSection load='4qkk' size='340' side='right' caption='[[4qkk]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~The entry~~ 4qkk is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qkk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QKK FirstGlance]. <br>
-	~~Authors~~: ~~Raiber, E~~.-A., ~~Murat~~, P., Chirgadze, D.Y., Luisi, B.F., ~~Balasubramanian~~, S.	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene></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=4qkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qkk RCSB], [http://www.ebi.ac.uk/pdbsum/4qkk PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of an oligonucleotide containing 5~~-~~formylcytosine~~	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Balasubramanian, S]]
		+	[[Category: Chirgadze, D Y]]
		+	[[Category: Luisi, B F]]
		+	[[Category: Murat, P]]
		+	[[Category: Raiber, E A]]
		+	[[Category: Dna]]
		+	[[Category: Epigenetic ten-eleven]]
		+	[[Category: Formylcytosine]]
		+	[[Category: Oligonucleotide]]
		+	[[Category: Thymine dna glycosylase]]
		+	[[Category: Translocation protein]]

OCA at 08:11, 24 September 2014

OCA — Wed, 24 Sep 2014 08:11:54 GMT

←Older revision		Revision as of 08:11, 24 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Raiber, E.-A., Murat, P., Chirgadze, D.Y., Luisi, B.F., Balasubramanian, S.		Authors: Raiber, E.-A., Murat, P., Chirgadze, D.Y., Luisi, B.F., Balasubramanian, S.

	Description: Crystal structure of an oligonucleotide containing 5-formylcytosine		Description: Crystal structure of an oligonucleotide containing 5-formylcytosine

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

OCA — Wed, 18 Jun 2014 06:38:31 GMT

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

←Older revision

Revision as of 06:38, 18 June 2014

OCA: New page: '''Unreleased structure''' The entry 4qkk is ON HOLD Authors: Raiber, E.-A., Murat, P., Chirgadze, D.Y., Luisi, B.F., Balasubramanian, S. Description: Crystal structure of an oligonucl...

OCA — Wed, 18 Jun 2014 06:38:30 GMT

New page: '''Unreleased structure''' The entry 4qkk is ON HOLD Authors: Raiber, E.-A., Murat, P., Chirgadze, D.Y., Luisi, B.F., Balasubramanian, S. Description: Crystal structure of an oligonucl...

New page

'''Unreleased structure'''

The entry 4qkk is ON HOLD

Authors: Raiber, E.-A., Murat, P., Chirgadze, D.Y., Luisi, B.F., Balasubramanian, S.

Description: Crystal structure of an oligonucleotide containing 5-formylcytosine