5z9z - Revision history

OCA at 08:37, 3 October 2018

OCA — Wed, 03 Oct 2018 08:37:05 GMT

←Older revision		Revision as of 08:37, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='5z9z' size='340' side='right' caption='[[5z9z]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5z9z' size='340' side='right' caption='[[5z9z]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z9z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z9Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z9z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z9Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SDN1, At3g50100, F3A4.180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5z9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z9z OCA], [http://pdbe.org/5z9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z9z RCSB], [http://www.ebi.ac.uk/pdbsum/5z9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z9z 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=5z9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z9z OCA], [http://pdbe.org/5z9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z9z RCSB], [http://www.ebi.ac.uk/pdbsum/5z9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z9z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SDN1_ARATH SDN1_ARATH]] 3'-5' exonuclease degrading single-stranded small RNAs.<ref>PMID:18787168</ref>		[[http://www.uniprot.org/uniprot/SDN1_ARATH SDN1_ARATH]] 3'-5' exonuclease degrading single-stranded small RNAs.<ref>PMID:18787168</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A family of DEDDh 3'-->5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3' end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3' end trimming mechanism for 3'-->5' exonucleases in the metabolism of small non-coding RNAs.
		+
		+	Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.,Chen J, Liu L, You C, Gu J, Ruan W, Zhang L, Gan J, Cao C, Huang Y, Chen X, Ma J Nat Commun. 2018 Sep 4;9(1):3585. doi: 10.1038/s41467-018-05942-7. PMID:30181559<ref>PMID:30181559</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5z9z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Cao, C]]		[[Category: Cao, C]]
	[[Category: Chen, J]]		[[Category: Chen, J]]

OCA at 05:32, 27 June 2018

OCA — Wed, 27 Jun 2018 05:32:26 GMT

←Older revision		Revision as of 05:32, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5z9z ~~is ON HOLD until Feb~~ 05 ~~2020~~	+	==The C-terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 (E329A/E330A/E332A)==
-		+	<StructureSection load='5z9z' size='340' side='right' caption='[[5z9z]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors~~: ~~Chen, J~~.~~, Liu, L~~.~~, You, C~~.~~, Gu, J~~.~~, Ruan, W~~.~~, Zhang, L~~.~~, Cao, C~~., ~~Gan, J~~., ~~Huang, Y~~., ~~Chen, X~~., ~~Ma, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5z9z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z9Z FirstGlance]. <br>
-	~~Description~~: ~~The C~~-~~terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 (E329A~~/~~E330A~~/~~E332A)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5z9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z9z OCA], [http://pdbe.org/5z9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z9z RCSB], [http://www.ebi.ac.uk/pdbsum/5z9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z9z ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SDN1_ARATH SDN1_ARATH]] 3'-5' exonuclease degrading single-stranded small RNAs.<ref>PMID:18787168</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cao, C]]		[[Category: Cao, C]]
-	[[Category: Gan, J]]
-	[[Category: Ruan, W]]
-	[[Category: Liu, L]]
	[[Category: Chen, J]]		[[Category: Chen, J]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
		+	[[Category: Gan, J]]
	[[Category: Gu, J]]		[[Category: Gu, J]]
-	[[Category: ~~Zhang~~, L]]	+	[[Category: Huang, Y]]
		+	[[Category: Liu, L]]
	[[Category: Ma, J]]		[[Category: Ma, J]]
		+	[[Category: Ruan, W]]
	[[Category: You, C]]		[[Category: You, C]]
-	[[Category: ~~Huang~~, Y]]	+	[[Category: Zhang, L]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna recognition motif]]

OCA at 03:50, 20 June 2018

OCA — Wed, 20 Jun 2018 03:50:42 GMT

←Older revision		Revision as of 03:50, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z9z is ON HOLD	+	The entry 5z9z is ON HOLD until Feb 05 2020

	Authors: Chen, J., Liu, L., You, C., Gu, J., Ruan, W., Zhang, L., Cao, C., Gan, J., Huang, Y., Chen, X., Ma, J.		Authors: Chen, J., Liu, L., You, C., Gu, J., Ruan, W., Zhang, L., Cao, C., Gan, J., Huang, Y., Chen, X., Ma, J.

OCA: Protected "5z9z" [edit=sysop:move=sysop]

OCA — Thu, 15 Feb 2018 05:10:46 GMT

Protected "5z9z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:10, 15 February 2018

OCA: New page: '''Unreleased structure''' The entry 5z9z is ON HOLD Authors: Chen, J., Liu, L., You, C., Gu, J., Ruan, W., Zhang, L., Cao, C., Gan, J., Huang, Y., Chen, X., Ma, J. Description: The C-...

OCA — Thu, 15 Feb 2018 05:10:45 GMT

New page: '''Unreleased structure''' The entry 5z9z is ON HOLD Authors: Chen, J., Liu, L., You, C., Gu, J., Ruan, W., Zhang, L., Cao, C., Gan, J., Huang, Y., Chen, X., Ma, J. Description: The C-...

New page

'''Unreleased structure'''

The entry 5z9z is ON HOLD

Authors: Chen, J., Liu, L., You, C., Gu, J., Ruan, W., Zhang, L., Cao, C., Gan, J., Huang, Y., Chen, X., Ma, J.

Description: The C-terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 (E329A/E330A/E332A)
[[Category: Unreleased Structures]]
[[Category: Cao, C]]
[[Category: Gan, J]]
[[Category: Ruan, W]]
[[Category: Liu, L]]
[[Category: Chen, J]]
[[Category: Chen, X]]
[[Category: Gu, J]]
[[Category: Zhang, L]]
[[Category: Ma, J]]
[[Category: You, C]]
[[Category: Huang, Y]]