5ygb - Revision history

OCA at 08:29, 22 November 2023

2023-11-22T08:29:23Z

←Older revision		Revision as of 08:29, 22 November 2023
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	==Crystal structure of drosophila melanogaster Papi extended Tudor domain mutant - D287A==		==Crystal structure of drosophila melanogaster Papi extended Tudor domain mutant - D287A==
-	<StructureSection load='5ygb' size='340' side='right' caption='[[5ygb]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5ygb' size='340' side='right'caption='[[5ygb]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YGB FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~papi~~, ~~Dmel\CG7082, PAPI, Papi, CG7082, Dmel_CG7082 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=7227 DROME])~~</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]] 1.4Å</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=5ygb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygb OCA], [~~http~~://pdbe.org/5ygb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ygb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ygb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygb 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=5ygb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygb OCA], [https://pdbe.org/5ygb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ygb RCSB], [https://www.ebi.ac.uk/pdbsum/5ygb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TDRKH_DROME TDRKH_DROME] Involved in the piwi-interacting RNA (piRNA) metabolic process, which 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 transposons which is essential for germline integrity (PubMed:21447556, PubMed:29531043). Likely to act by recruiting Piwi proteins such as AGO3 and piwi to the piRNA biogenesis machinery in the nuage (PubMed:21447556, PubMed:29531043). Required for the final steps of primary piRNA biogenesis by participating in the 3' end-trimming of piwi-bound intermediates into mature piRNAs (PubMed:29531043).<ref>PMID:21447556</ref> <ref>PMID:29531043</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: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
-	[[Category: ~~Huang, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zhang,~~ Y H]]	+	[[Category: Huang Y]]
-	[[Category: ~~Extended tudor domain]]~~	+	[[Category: Zhang YH]]
-	~~[[Category: Pirna pathway]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 14:14, 11 April 2018

2018-04-11T14:14:25Z

←Older revision		Revision as of 14:14, 11 April 2018
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	<StructureSection load='5ygb' size='340' side='right' caption='[[5ygb]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5ygb' size='340' side='right' caption='[[5ygb]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGB FirstGlance]. <br>
-	</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=5ygb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygb OCA], [http://pdbe.org/5ygb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygb RCSB], [http://www.ebi.ac.uk/pdbsum/5ygb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygb ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">papi, Dmel\CG7082, PAPI, Papi, CG7082, Dmel_CG7082 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=5ygb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygb OCA], [http://pdbe.org/5ygb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygb RCSB], [http://www.ebi.ac.uk/pdbsum/5ygb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Tudor domain-containing (Tdrd) family proteins play a critical role in transposon silencing in animal gonads by recognizing the symmetrically dimethylated arginine (sDMA) on the (G/A)R motif of the N-terminal of PIWI family proteins via the eTud domains. Papi, also known as "Tdrd2," is involved in Zucchini-mediated PIWI-interacting RNA (piRNA) 3'-end maturation. Intriguingly, a recent study showed that, in papi mutant flies, only Piwi-bound piRNAs increased in length, and not Ago3-bound or Aub-bound piRNAs. However, the molecular and structural basis of the Papi-Piwi complex is still not fully understood, which limits mechanistic understanding of the function of Papi in piRNA biogenesis. In the present study, we determined the crystal structures of Papi-eTud in the apo form and in complex with a peptide containing unmethylated or dimethylated R10 residues. Structural and biochemical analysis showed that the Papi interaction region on the Drosophila Piwi contains an RGRRR motif (R7-R11) distinct from the consensus (G/A)R motif recognized by canonical eTud. Mass spectrometry results indicated that Piwi is the major binding partner of Papi in vivo. The papi mutant flies suffered from both fertility and transposon-silencing defects, supporting the important role conferred to Papi in piRNA 3' processing through direct interaction with Piwi proteins.
		+
		+	Structural insights into the sequence-specific recognition of Piwi by Drosophila Papi.,Zhang Y, Liu W, Li R, Gu J, Wu P, Peng C, Ma J, Wu L, Yu Y, Huang Y Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3374-3379. doi:, 10.1073/pnas.1717116115. Epub 2018 Mar 12. PMID:29531043<ref>PMID:29531043</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ygb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Huang, Y]]		[[Category: Huang, Y]]
	[[Category: Zhang, Y H]]		[[Category: Zhang, Y H]]

OCA at 06:27, 14 March 2018

2018-03-14T06:27:03Z

←Older revision		Revision as of 06:27, 14 March 2018
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-	'''Unreleased structure'''

-	~~The entry 5ygb is ON HOLD until Paper Publication~~	+	==Crystal structure of drosophila melanogaster Papi extended Tudor domain mutant - D287A==
-		+	<StructureSection load='5ygb' size='340' side='right' caption='[[5ygb]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors: Zhang, Y.H., Huang, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ygb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGB FirstGlance]. <br>
-	~~Description:~~ Crystal structure of drosophila melanogaster Papi extended Tudor domain mutant -D287A	+	</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=5ygb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygb OCA], [http://pdbe.org/5ygb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygb RCSB], [http://www.ebi.ac.uk/pdbsum/5ygb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygb ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Zhang~~, Y.H]]	+	__TOC__
		+	</StructureSection>
	[[Category: Huang, Y]]		[[Category: Huang, Y]]
		+	[[Category: Zhang, Y H]]
		+	[[Category: Extended tudor domain]]
		+	[[Category: Pirna pathway]]
		+	[[Category: Protein binding]]

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

2017-10-04T08:03:05Z

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

←Older revision

Revision as of 08:03, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ygb is ON HOLD until Paper Publication Authors: Zhang, Y.H., Huang, Y. Description: Crystal structure of drosophila melanogaster Papi extended Tud...

2017-10-04T08:03:04Z

New page: '''Unreleased structure''' The entry 5ygb is ON HOLD until Paper Publication Authors: Zhang, Y.H., Huang, Y. Description: Crystal structure of drosophila melanogaster Papi extended Tud...

New page

'''Unreleased structure'''

The entry 5ygb is ON HOLD until Paper Publication

Authors: Zhang, Y.H., Huang, Y.

Description: Crystal structure of drosophila melanogaster Papi extended Tudor domain mutant -D287A
[[Category: Unreleased Structures]]
[[Category: Zhang, Y.H]]
[[Category: Huang, Y]]