3vna - Revision history

OCA at 08:40, 20 March 2024

2024-03-20T08:40:48Z

←Older revision		Revision as of 08:40, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3vna' size='340' side='right'caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3vna' size='340' side='right'caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vna]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VNA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vna]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VNA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3vnb\|3vnb]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [https://pdbe.org/3vna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [https://www.ebi.ac.uk/pdbsum/3vna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vna 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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [https://pdbe.org/3vna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [https://www.ebi.ac.uk/pdbsum/3vna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vna ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AGO1_ARATH AGO1_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>	+	[https://www.uniprot.org/uniprot/AGO1_ARATH AGO1_ARATH] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The RISC-associated Argonaute (Ago) proteins play the catalytic role for RISC-mediated gene regulation by selecting small RNAs and subsequent targeting and cleavage of complementary mRNAs. Ago Mid domains are proposed to play essential roles in small RNA sorting. Here, we report the crystal structures of Arabidopsis Ago1 Mid domain and its chimera mutant with part of Ago1 replaced by Ago4. The structures demonstrate that a single amino insertion in the nucleotide specificity loop of AtAgo1 will change the nucleotide binding preference of AtAgo1 from "5'-U" to "5'-A". Moreover, we identify a long positively charged groove located along the "5'-end-nucleotide specificity loop" and occupied by several sulfate ions with the distance of 9-11A distance, indicating a putative mRNA target binding groove.	+
-		+
-	Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains.,Zha X, Xia Q, Adam Yuan Y FEBS Lett. 2012 Sep 21;586(19):3200-7. doi: 10.1016/j.febslet.2012.06.038. Epub, 2012 Jul 3. PMID:22771475<ref>PMID:22771475</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3vna" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 26:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Yuan~~, Y A~~]]	+	[[Category: Yuan YA]]
-	[[Category: Zha, X]]	+	[[Category: Zha X]]
-	~~[[Category: 5'-nucleotide small rna binding]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 18:53, 27 July 2022

2022-07-27T18:53:53Z

←Older revision		Revision as of 18:53, 27 July 2022
Line 1:		Line 1:

	==Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains==		==Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains==
-	<StructureSection load='3vna' size='340' side='right' caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3vna' size='340' side='right'caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vna]] 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=3VNA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VNA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vna]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VNA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vnb\|3vnb]]</div></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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [~~http~~://pdbe.org/3vna PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vna PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vna 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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [https://pdbe.org/3vna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [https://www.ebi.ac.uk/pdbsum/3vna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vna ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AGO1_ARATH AGO1_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>	+	[[https://www.uniprot.org/uniprot/AGO1_ARATH AGO1_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Argonaute\|Argonaute]]	+	*[[Argonaute 3D structures\|Argonaute 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Yuan, Y A]]		[[Category: Yuan, Y A]]
	[[Category: Zha, X]]		[[Category: Zha, X]]

OCA at 07:15, 4 August 2016

2016-08-04T07:15:12Z

←Older revision		Revision as of 07:15, 4 August 2016
Line 1:		Line 1:
		+
	==Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains==		==Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains==
	<StructureSection load='3vna' size='340' side='right' caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3vna' size='340' side='right' caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [http://www.ebi.ac.uk/pdbsum/3vna 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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [http://pdbe.org/3vna PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [http://www.ebi.ac.uk/pdbsum/3vna PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vna ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3vna" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 06:49, 25 December 2014

2014-12-25T06:49:49Z

←Older revision		Revision as of 06:49, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vna]] 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=3VNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VNA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vna]] 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=3VNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VNA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [http://www.ebi.ac.uk/pdbsum/3vna 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=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [http://www.ebi.ac.uk/pdbsum/3vna PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AGO1_ARATH AGO1_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
-	[[Category: Yuan, Y A.]]	+	[[Category: Yuan, Y A]]
-	[[Category: Zha, X.]]	+	[[Category: Zha, X]]
	[[Category: 5'-nucleotide small rna binding]]		[[Category: 5'-nucleotide small rna binding]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 10:43, 16 July 2014

2014-07-16T10:43:50Z

←Older revision		Revision as of 10:43, 16 July 2014
Line 1:		Line 1:
-	[[~~Image:~~3vna.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains==
		+	<StructureSection load='3vna' size='340' side='right' caption='[[3vna]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vna]] 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=3VNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VNA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vnb\|3vnb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vna RCSB], [http://www.ebi.ac.uk/pdbsum/3vna PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RISC-associated Argonaute (Ago) proteins play the catalytic role for RISC-mediated gene regulation by selecting small RNAs and subsequent targeting and cleavage of complementary mRNAs. Ago Mid domains are proposed to play essential roles in small RNA sorting. Here, we report the crystal structures of Arabidopsis Ago1 Mid domain and its chimera mutant with part of Ago1 replaced by Ago4. The structures demonstrate that a single amino insertion in the nucleotide specificity loop of AtAgo1 will change the nucleotide binding preference of AtAgo1 from "5'-U" to "5'-A". Moreover, we identify a long positively charged groove located along the "5'-end-nucleotide specificity loop" and occupied by several sulfate ions with the distance of 9-11A distance, indicating a putative mRNA target binding groove.

-	~~{{STRUCTURE_3vna\| PDB=3vna \| SCENE= }}~~	+	Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains.,Zha X, Xia Q, Adam Yuan Y FEBS Lett. 2012 Sep 21;586(19):3200-7. doi: 10.1016/j.febslet.2012.06.038. Epub, 2012 Jul 3. PMID:22771475<ref>PMID:22771475</ref>

-	~~===Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22771475}}~~	+	==See Also==
-		+	*[[Argonaute\|Argonaute]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3vna~~]] ~~is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=3VNA OCA~~].	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arath]]
	[[Category: Yuan, Y A.]]		[[Category: Yuan, Y A.]]
	[[Category: Zha, X.]]		[[Category: Zha, X.]]

OCA at 07:16, 10 October 2012

2012-10-10T07:16:23Z

←Older revision		Revision as of 07:16, 10 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3vna.jpg\|left\|200px]]

-	~~The entry~~ 3vna ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3vna\| PDB=3vna \| SCENE= }}

-	~~Authors: Yuan, Y.A., Zha, X.~~	+	===Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains===

-	~~Description~~: ~~Structural insights into~~ small ~~RNA sorting and mRNA~~ binding ~~by Arabidopsis Ago Mid domains~~	+	{{ABSTRACT_PUBMED_22771475}}
		+
		+	==About this Structure==
		+	[[3vna]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNA OCA].
		+	[[Category: Yuan, Y A.]]
		+	[[Category: Zha, X.]]
		+	[[Category: 5'-nucleotide small rna binding]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rossmann fold]]

OCA at 19:54, 26 September 2012

2012-09-26T19:54:30Z

←Older revision		Revision as of 19:54, 26 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vna is ON HOLD	+	The entry 3vna is ON HOLD until Paper Publication

	Authors: Yuan, Y.A., Zha, X.		Authors: Yuan, Y.A., Zha, X.

	Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains		Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains

OCA at 06:54, 1 February 2012

2012-02-01T06:54:33Z

←Older revision		Revision as of 06:54, 1 February 2012
Line 3:		Line 3:
	The entry 3vna is ON HOLD		The entry 3vna is ON HOLD

-	Authors: Yuan, Y. A., Zha, X	+	Authors: Yuan, Y.A., Zha, X.

	Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains		Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains

OCA: Protected "3vna" [edit=sysop:move=sysop]

2012-01-18T10:23:25Z

Protected "3vna" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:23, 18 January 2012

OCA: New page: '''Unreleased structure''' The entry 3vna is ON HOLD Authors: Yuan, Y. A., Zha, X Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domain...

2012-01-18T10:23:24Z

New page: '''Unreleased structure''' The entry 3vna is ON HOLD Authors: Yuan, Y. A., Zha, X Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domain...

New page

'''Unreleased structure'''

The entry 3vna is ON HOLD

Authors: Yuan, Y. A., Zha, X

Description: Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago Mid domains