5js2 - Revision history

OCA at 19:04, 20 September 2023

2023-09-20T19:04:13Z

← Older revision		Revision as of 19:04, 20 September 2023
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	<StructureSection load='5js2' size='340' side='right'caption='[[5js2]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='5js2' size='340' side='right'caption='[[5js2]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IPH:PHENOL'>IPH</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.954Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NW:2-O-METHYL-5-O-THIOPHOSPHONOADENOSINE'>6NW</scene>, <scene name='pdbligand=6OO:2-O-METHYL-5-O-THIOPHOSPHONOCYTIDINE'>6OO</scene>, <scene name='pdbligand=6OP:1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>6OP</scene>, <scene name='pdbligand=F2T:2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONOURIDINE'>F2T</scene>, <scene name='pdbligand=~~UFT~~:~~2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)~~'>~~UFT~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NW:2-O-METHYL-5-O-THIOPHOSPHONOADENOSINE'>6NW</scene>, <scene name='pdbligand=6OO:2-O-METHYL-5-O-THIOPHOSPHONOCYTIDINE'>6OO</scene>, <scene name='pdbligand=6OP:1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>6OP</scene>, <scene name='pdbligand=F2T:2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONOURIDINE'>F2T</scene>, <scene name='pdbligand=IPH:PHENOL'>IPH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"~~>~~[[5js1\|5js1]]~~</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=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [https://pdbe.org/5js2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [https://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AGO2, EIF2C2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [~~http~~://pdbe.org/5js2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/AGO2_HUMAN AGO2_HUMAN]] Required for RNA-mediated gene silencing (RNAi) by the RNA-induced silencing complex (RISC). The 'minimal RISC' appears to include EIF2C2/AGO2 bound to a short guide RNA such as a microRNA (miRNA) or short interfering RNA (siRNA). These guide RNAs direct RISC to complementary mRNAs that are targets for RISC-mediated gene silencing. The precise mechanism of gene silencing depends on the degree of complementarity between the miRNA or siRNA and its target. Binding of RISC to a perfectly complementary mRNA generally results in silencing due to endonucleolytic cleavage of the mRNA specifically by EIF2C2/AGO2. Binding of RISC to a partially complementary mRNA results in silencing through inhibition of translation, and this is independent of endonuclease activity. May inhibit translation initiation by binding to the 7-methylguanosine cap, thereby preventing the recruitment of the translation initiation factor eIF4-E. May also inhibit translation initiation via interaction with EIF6, which itself binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The inhibition of translational initiation leads to the accumulation of the affected mRNA in cytoplasmic processing bodies (P-bodies), where mRNA degradation may subsequently occur. In some cases RISC-mediated translational repression is also observed for miRNAs that perfectly match the 3' untranslated region (3'-UTR). Can also up-regulate the translation of specific mRNAs under certain growth conditions. Binds to the AU element of the 3'-UTR of the TNF (TNF-alpha) mRNA and up-regulates translation under conditions of serum starvation. Also required for transcriptional gene silencing (TGS), in which short RNAs known as antigene RNAs or agRNAs direct the transcriptional repression of complementary promoter regions.<ref>PMID:15105377</ref> <ref>PMID:15260970</ref> <ref>PMID:15337849</ref> <ref>PMID:15284456</ref> <ref>PMID:16271387</ref> <ref>PMID:16289642</ref> <ref>PMID:16142218</ref> <ref>PMID:16357216</ref> <ref>PMID:15800637</ref> <ref>PMID:16081698</ref> <ref>PMID:16936728</ref> <ref>PMID:16756390</ref> <ref>PMID:17382880</ref> <ref>PMID:17524464</ref> <ref>PMID:17932509</ref> <ref>PMID:17531811</ref> <ref>PMID:17507929</ref> <ref>PMID:18048652</ref> <ref>PMID:18771919</ref> <ref>PMID:18690212</ref> <ref>PMID:18178619</ref> <ref>PMID:19167051</ref>		[https://www.uniprot.org/uniprot/AGO2_HUMAN AGO2_HUMAN] Required for RNA-mediated gene silencing (RNAi) by the RNA-induced silencing complex (RISC). The 'minimal RISC' appears to include EIF2C2/AGO2 bound to a short guide RNA such as a microRNA (miRNA) or short interfering RNA (siRNA). These guide RNAs direct RISC to complementary mRNAs that are targets for RISC-mediated gene silencing. The precise mechanism of gene silencing depends on the degree of complementarity between the miRNA or siRNA and its target. Binding of RISC to a perfectly complementary mRNA generally results in silencing due to endonucleolytic cleavage of the mRNA specifically by EIF2C2/AGO2. Binding of RISC to a partially complementary mRNA results in silencing through inhibition of translation, and this is independent of endonuclease activity. May inhibit translation initiation by binding to the 7-methylguanosine cap, thereby preventing the recruitment of the translation initiation factor eIF4-E. May also inhibit translation initiation via interaction with EIF6, which itself binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The inhibition of translational initiation leads to the accumulation of the affected mRNA in cytoplasmic processing bodies (P-bodies), where mRNA degradation may subsequently occur. In some cases RISC-mediated translational repression is also observed for miRNAs that perfectly match the 3' untranslated region (3'-UTR). Can also up-regulate the translation of specific mRNAs under certain growth conditions. Binds to the AU element of the 3'-UTR of the TNF (TNF-alpha) mRNA and up-regulates translation under conditions of serum starvation. Also required for transcriptional gene silencing (TGS), in which short RNAs known as antigene RNAs or agRNAs direct the transcriptional repression of complementary promoter regions.<ref>PMID:15105377</ref> <ref>PMID:15260970</ref> <ref>PMID:15337849</ref> <ref>PMID:15284456</ref> <ref>PMID:16271387</ref> <ref>PMID:16289642</ref> <ref>PMID:16142218</ref> <ref>PMID:16357216</ref> <ref>PMID:15800637</ref> <ref>PMID:16081698</ref> <ref>PMID:16936728</ref> <ref>PMID:16756390</ref> <ref>PMID:17382880</ref> <ref>PMID:17524464</ref> <ref>PMID:17932509</ref> <ref>PMID:17531811</ref> <ref>PMID:17507929</ref> <ref>PMID:18048652</ref> <ref>PMID:18771919</ref> <ref>PMID:18690212</ref> <ref>PMID:18178619</ref> <ref>PMID:19167051</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~MacRae, I J~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Schirle, N T~~]]		[[Category: MacRae IJ]]
	[[Category: ~~Argonaute]]~~		[[Category: Schirle NT]]
	~~[[Category: Hydrolase-rna complex]]~~
	~~[[Category: Nuclease]]~~
	~~[[Category: Rnai]]~~
	~~[[Category: Sirna~~]]

OCA at 11:35, 17 June 2020

2020-06-17T11:35:52Z

← Older revision		Revision as of 11:35, 17 June 2020
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	==Human Argonaute-2 Bound to a Modified siRNA==		==Human Argonaute-2 Bound to a Modified siRNA==
	<StructureSection load='5js2' size='340' side='right' caption='[[5js2]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='5js2' size='340' side='right'caption='[[5js2]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPH:PHENOL'>IPH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPH:PHENOL'>IPH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NW:2-O-METHYL-5-O-THIOPHOSPHONOADENOSINE'>6NW</scene>, <scene name='pdbligand=6OO:2-O-METHYL-5-O-THIOPHOSPHONOCYTIDINE'>6OO</scene>, <scene name='pdbligand=6OP:1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>6OP</scene>, <scene name='pdbligand=F2T:2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONOURIDINE'>F2T</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NW:2-O-METHYL-5-O-THIOPHOSPHONOADENOSINE'>6NW</scene>, <scene name='pdbligand=6OO:2-O-METHYL-5-O-THIOPHOSPHONOCYTIDINE'>6OO</scene>, <scene name='pdbligand=6OP:1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>6OP</scene>, <scene name='pdbligand=F2T:2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONOURIDINE'>F2T</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5js1\|5js1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5js1\|5js1]]</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=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [http://pdbe.org/5js2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [http://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AGO2, EIF2C2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [http://pdbe.org/5js2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [http://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5js2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5js2" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Argonaute 3D structures\|Argonaute 3D structures]]
			*[[Eukaryotic initiation factor 3D structures\|Eukaryotic initiation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: MacRae, I J]]		[[Category: MacRae, I J]]
	[[Category: Schirle, N T]]		[[Category: Schirle, N T]]

OCA at 15:18, 26 July 2016

2016-07-26T15:18:33Z

@@ Line 1: / Line 1: @@
-The entry 5js2 is ON HOLD  until Paper Publication
+==Human Argonaute-2 Bound to a Modified siRNA==
-Authors:
+Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.,Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ J Am Chem Soc. 2016 Jul 20;138(28):8694-7. doi: 10.1021/jacs.6b04454. Epub 2016, Jul 12. PMID:27380263<ref>PMID:27380263</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>

OCA at 23:37, 12 July 2016

2016-07-12T23:37:53Z

← Older revision		Revision as of 23:37, 12 July 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5js2 is ON HOLD		The entry 5js2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5js2" [edit=sysop:move=sysop]

2016-06-01T13:45:38Z

Protected "5js2" [edit=sysop:move=sysop]

← Older revision	Revision as of 13:45, 1 June 2016
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5js2 is ON HOLD Authors: Description: Category: Unreleased Structures

2016-06-01T13:45:37Z

New page: '''Unreleased structure''' The entry 5js2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5js2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]