5hn2 - Revision history

OCA at 10:47, 16 August 2023

2023-08-16T10:47:38Z

←Older revision		Revision as of 10:47, 16 August 2023
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	<StructureSection load='5hn2' size='340' side='right'caption='[[5hn2]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5hn2' size='340' side='right'caption='[[5hn2]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HN2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn2]] is a 6 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=5HN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HN2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5hn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn2 OCA], [~~http~~://pdbe.org/5hn2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hn2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hn2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn2 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=5hn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn2 OCA], [https://pdbe.org/5hn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hn2 RCSB], [https://www.ebi.ac.uk/pdbsum/5hn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn2 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: ~~Luo, Z P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Sheng, J~~]]	+	[[Category: Luo ZP]]
-	[[Category: ~~5-formylcytosine]]~~	+	[[Category: Sheng J]]
-	~~[[Category: Rna~~]]	+

OCA at 08:24, 27 May 2020

2020-05-27T08:24:30Z

←Older revision		Revision as of 08:24, 27 May 2020
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	==Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex==		==Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex==
-	<StructureSection load='5hn2' size='340' side='right' caption='[[5hn2]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5hn2' size='340' side='right'caption='[[5hn2]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HN2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HN2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</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=5hn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn2 OCA], [http://pdbe.org/5hn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn2 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn2 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn2 OCA], [http://pdbe.org/5hn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn2 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn2 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: Luo, Z P]]		[[Category: Luo, Z P]]
	[[Category: Sheng, J]]		[[Category: Sheng, J]]
	[[Category: 5-formylcytosine]]		[[Category: 5-formylcytosine]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 12:06, 13 May 2016

2016-05-13T12:06:25Z

←Older revision		Revision as of 12:06, 13 May 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5hn2 is ~~ON HOLD until Paper~~ Publication	+	==Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex==
		+	<StructureSection load='5hn2' size='340' side='right' caption='[[5hn2]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hn2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</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=5hn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn2 OCA], [http://pdbe.org/5hn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn2 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn2 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5'-GUA(f5C)GUAC-3']2that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex.

-	~~Authors: Luo~~, Z~~.P.~~, ~~Sheng~~, J.	+	Base pairing and structural insights into the 5-formylcytosine in RNA duplex.,Wang R, Luo Z, He K, Delaney MO, Chen D, Sheng J Nucleic Acids Res. 2016 Apr 13. pii: gkw235. PMID:27079978<ref>PMID:27079978</ref>

-	~~Description: Base Pairing and Structure Insights into~~ the ~~5-Formylcytosine in RNA Duplex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Luo, Z.P]]	+	<div class="pdbe-citations 5hn2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Luo, Z P]]
	[[Category: Sheng, J]]		[[Category: Sheng, J]]
		+	[[Category: 5-formylcytosine]]
		+	[[Category: Rna]]

OCA at 00:56, 21 February 2016

2016-02-21T00:56:26Z

←Older revision		Revision as of 00:56, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hn2 is ON HOLD	+	The entry 5hn2 is ON HOLD until Paper Publication

	Authors: Luo, Z.P., Sheng, J.		Authors: Luo, Z.P., Sheng, J.

OCA: Protected "5hn2" [edit=sysop:move=sysop]

2016-01-28T00:54:46Z

Protected "5hn2" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:54, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hn2 is ON HOLD Authors: Luo, Z.P., Sheng, J. Description: Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex [[Category: ...

2016-01-28T00:54:45Z

New page: '''Unreleased structure''' The entry 5hn2 is ON HOLD Authors: Luo, Z.P., Sheng, J. Description: Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex [[Category: ...

New page

'''Unreleased structure'''

The entry 5hn2 is ON HOLD

Authors: Luo, Z.P., Sheng, J.

Description: Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex
[[Category: Unreleased Structures]]
[[Category: Luo, Z.P]]
[[Category: Sheng, J]]