5fis - Revision history

OCA at 06:53, 19 July 2023

OCA — Wed, 19 Jul 2023 06:53:04 GMT

←Older revision		Revision as of 06:53, 19 July 2023
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	<StructureSection load='5fis' size='340' side='right'caption='[[5fis]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5fis' size='340' side='right'caption='[[5fis]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fis]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bommo Bommo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FIS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fis]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bombyx_mori Bombyx mori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FIS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</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]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5fiq\|5fiq]]~~</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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [https://pdbe.org/5fis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [https://www.ebi.ac.uk/pdbsum/5fis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fis ProSAT]</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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [~~http~~://pdbe.org/5fis PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fis PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fis ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/EXD1_BOMMO EXD1_BOMMO] RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity. The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing-triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease.<ref>PMID:26669262</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: ~~Bommo~~]]	+	[[Category: Bombyx mori]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, K M~~]]	+	[[Category: Chen KM]]
-	[[Category: Fauvarque~~, M O~~]]	+	[[Category: Fauvarque MO]]
-	[[Category: Homolka, D]]	+	[[Category: Homolka D]]
-	~~[[Category: Janeiro, B K.Rodino~~]]	+	[[Category: McCarthy AA]]
-	[[Category: McCarthy~~, A A~~]]	+	[[Category: Pandey RR]]
-	[[Category: Pandey~~, R R~~]]	+	[[Category: Pillai RS]]
-	[[Category: Pillai~~, R S~~]]	+	[[Category: Reuter M]]
-	[[Category: Reuter, M]]	+	[[Category: Rodino Janeiro BK]]
-	[[Category: ~~Sachidanandam, R~~]]	+	[[Category: Sachidanandam R]]
-	[[Category: ~~Yang, Z~~]]	+	[[Category: Yang Z]]
-	[[Category: ~~Dimer]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pirna biogenesis]]~~	+
-	~~[[Category: Rna binding~~]]	+

OCA at 07:21, 6 May 2020

OCA — Wed, 06 May 2020 07:21:28 GMT

←Older revision		Revision as of 07:21, 6 May 2020
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		+
	==Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation==		==Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation==
-	<StructureSection load='5fis' size='340' side='right' caption='[[5fis]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5fis' size='340' side='right'caption='[[5fis]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fis]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FIS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fis]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bommo Bommo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FIS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FIS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fiq\|5fiq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fiq\|5fiq]]</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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [http://pdbe.org/5fis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [http://www.ebi.ac.uk/pdbsum/5fis 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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [http://pdbe.org/5fis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [http://www.ebi.ac.uk/pdbsum/5fis PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fis ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5fis" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fis" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bommo]]
		+	[[Category: Large Structures]]
	[[Category: Chen, K M]]		[[Category: Chen, K M]]
	[[Category: Fauvarque, M O]]		[[Category: Fauvarque, M O]]

OCA at 12:29, 13 January 2016

OCA — Wed, 13 Jan 2016 12:29:18 GMT

←Older revision		Revision as of 12:29, 13 January 2016
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	<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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [http://pdbe.org/5fis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [http://www.ebi.ac.uk/pdbsum/5fis 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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [http://pdbe.org/5fis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [http://www.ebi.ac.uk/pdbsum/5fis PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a transcript by the cytosolic mouse PIWI protein MILI acts as a trigger to initiate its further 5'-->3' processing into non-overlapping fragments. These fragments accumulate as new piRNAs within both cytosolic MILI and the nuclear MIWI2. We also identify Exonuclease domain-containing 1 (EXD1) as a partner of the MIWI2 piRNA biogenesis factor TDRD12. EXD1 homodimers are inactive as a nuclease but function as an RNA adaptor within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 reduces sequences generated by MILI slicing, impacts biogenesis of MIWI2 piRNAs, and de-represses LINE1 retrotransposons. Thus, piRNA biogenesis triggered by PIWI slicing, and promoted by EXD1, ensures that the same guides instruct PIWI proteins in the nucleus and cytoplasm.
		+
		+	PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway.,Yang Z, Chen KM, Pandey RR, Homolka D, Reuter M, Janeiro BK, Sachidanandam R, Fauvarque MO, McCarthy AA, Pillai RS Mol Cell. 2016 Jan 7;61(1):138-52. doi: 10.1016/j.molcel.2015.11.009. Epub 2015, Dec 6. PMID:26669262<ref>PMID:26669262</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fis" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:50, 23 December 2015

OCA — Wed, 23 Dec 2015 12:50:57 GMT

←Older revision		Revision as of 12:50, 23 December 2015
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-	'''~~Unreleased structure~~'''	+	==Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation==
-		+	<StructureSection load='5fis' size='340' side='right' caption='[[5fis]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~The entry~~ 5fis is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fis]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FIS FirstGlance]. <br>
-	~~Authors~~: ~~Yang, Z~~.~~, Chen, K~~.M.~~, Pandey, R~~.R.~~, Homolka, D~~.~~, Reuter, M~~.~~, RodinoJaneiro, B~~.~~K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	~~Description~~: ~~Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fiq\|5fiq]]</td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5fis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fis OCA], [http://pdbe.org/5fis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fis RCSB], [http://www.ebi.ac.uk/pdbsum/5fis PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Fauvarque, M.O~~]]	+	</table>
-	[[~~Category~~: ~~Yang~~, Z]]	+	__TOC__
-	[[Category: ~~Reuter~~, M]]	+	</StructureSection>
-	[[Category: ~~Pillai~~, ~~R.S~~]]	+	[[Category: Chen, K M]]
		+	[[Category: Fauvarque, M O]]
	[[Category: Homolka, D]]		[[Category: Homolka, D]]
-	[[Category: ~~Chen~~, K.M]]	+	[[Category: Janeiro, B K.Rodino]]
		+	[[Category: McCarthy, A A]]
		+	[[Category: Pandey, R R]]
		+	[[Category: Pillai, R S]]
		+	[[Category: Reuter, M]]
	[[Category: Sachidanandam, R]]		[[Category: Sachidanandam, R]]
-	[[Category: ~~Mccarthy~~, ~~A.A~~]]	+	[[Category: Yang, Z]]
-	[[Category: ~~Pandey, R.R~~]]	+	[[Category: Dimer]]
-	[[Category: ~~Rodinojaneiro, B.K~~]]	+	[[Category: Exonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pirna biogenesis]]
		+	[[Category: Rna binding]]

OCA at 03:28, 1 December 2015

OCA — Tue, 01 Dec 2015 03:28:45 GMT

←Older revision		Revision as of 03:28, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S.		Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S.

OCA at 03:04, 16 October 2015

OCA — Fri, 16 Oct 2015 03:04:39 GMT

←Older revision		Revision as of 03:04, 16 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fis is ON HOLD ~~until sometime in the future~~	+	The entry 5fis is ON HOLD

	Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S.		Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S.

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

OCA — Wed, 07 Oct 2015 12:56:52 GMT

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

←Older revision

Revision as of 12:56, 7 October 2015

OCA: New page: '''Unreleased structure''' The entry 5fis is ON HOLD until sometime in the future Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidananda...

OCA — Wed, 07 Oct 2015 12:56:50 GMT

New page: '''Unreleased structure''' The entry 5fis is ON HOLD until sometime in the future Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidananda...

New page

'''Unreleased structure'''

The entry 5fis is ON HOLD until sometime in the future

Authors: Yang, Z., Chen, K.M., Pandey, R.R., Homolka, D., Reuter, M., RodinoJaneiro, B.K., Sachidanandam, R., Fauvarque, M.O., McCarthy, A.A., Pillai, R.S.

Description: Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation
[[Category: Unreleased Structures]]
[[Category: Fauvarque, M.O]]
[[Category: Yang, Z]]
[[Category: Reuter, M]]
[[Category: Pillai, R.S]]
[[Category: Homolka, D]]
[[Category: Chen, K.M]]
[[Category: Sachidanandam, R]]
[[Category: Mccarthy, A.A]]
[[Category: Pandey, R.R]]
[[Category: Rodinojaneiro, B.K]]