4zg0 - Revision history

OCA at 15:44, 8 November 2023

OCA — Wed, 08 Nov 2023 15:44:05 GMT

←Older revision		Revision as of 15:44, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>
-	</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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [https://pdbe.org/4zg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [https://www.ebi.ac.uk/pdbsum/4zg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zg0 ProSAT]</span></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]] 2.006Å</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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [https://pdbe.org/4zg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [https://www.ebi.ac.uk/pdbsum/4zg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zg0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:26, 18 May 2023

OCA — Thu, 18 May 2023 07:26:21 GMT

←Older revision		Revision as of 07:26, 18 May 2023
Line 1:		Line 1:

	==Crystal structure of Mouse Syndesmos protein==		==Crystal structure of Mouse Syndesmos protein==
-	<StructureSection load='4zg0' size='340' side='right' caption='[[4zg0]], [[Resolution\|resolution]] 2.01Å' scene=''>	+	<StructureSection load='4zg0' size='340' side='right'caption='[[4zg0]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nudt16l1, Sdos ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	</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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [https://pdbe.org/4zg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [https://www.ebi.ac.uk/pdbsum/4zg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zg0 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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [~~http~~://pdbe.org/4zg0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zg0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zg0 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~SDOS_MOUSE SDOS_MOUSE~~]~~] Does not play a role in U8 snoRNA decapping activity~~. ~~Binds U8 snoRNA~~ (~~By similarity~~). ~~Probable adapter protein~~, ~~which may link syndecan~~-~~4 (SDC4)~~ and ~~paxilin (TGFB1I1~~ and ~~PXN~~) ~~receptors~~.	+	[https://www.uniprot.org/uniprot/TIRR_MOUSE TIRR_MOUSE] Key regulator of TP53BP1 required to stabilize TP53BP1 and regulate its recruitment to chromatin. In absence of DNA damage, interacts with the tandem Tudor-like domain of TP53BP1, masking the region that binds histone H4 dimethylated at 'Lys-20' (H4K20me2), thereby preventing TP53BP1 recruitment to chromatin and maintaining TP53BP1 localization to the nucleus. Following DNA damage, ATM-induced phosphorylation of TP53BP1 and subsequent recruitment of RIF1 leads to dissociate NUDT16L1/TIRR from TP53BP1, unmasking the tandem Tudor-like domain and allowing recruitment of TP53BP1 to DNA double strand breaks (DSBs). Binds U8 snoRNA.[UniProtKB:Q9BRJ7]
	<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: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: Cho, H]]	+	[[Category: Mus musculus]]
-	[[Category: Kim, H]]	+	[[Category: Cho H]]
-	[[Category: Lee, I]]	+	[[Category: Kim H]]
-	[[Category: Lee, W]]	+	[[Category: Lee I]]
-	[[Category: Yoo, J]]	+	[[Category: Lee W]]
-	~~[[Category: Cytoplasmic protein]]~~	+	[[Category: Yoo J]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nudix hydrolase]]~~	+
-	~~[[Category: Syndecan-4 cytoplasmic domain interactor~~]]	+

OCA at 12:26, 16 November 2017

OCA — Thu, 16 Nov 2017 12:26:30 GMT

←Older revision		Revision as of 12:26, 16 November 2017
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	<StructureSection load='4zg0' size='340' side='right' caption='[[4zg0]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='4zg0' size='340' side='right' caption='[[4zg0]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZG0 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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [http://pdbe.org/4zg0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [http://www.ebi.ac.uk/pdbsum/4zg0 PDBsum]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nudt16l1, Sdos ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [http://pdbe.org/4zg0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [http://www.ebi.ac.uk/pdbsum/4zg0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zg0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Cho, H]]		[[Category: Cho, H]]
	[[Category: Kim, H]]		[[Category: Kim, H]]

OCA at 08:18, 1 June 2016

OCA — Wed, 01 Jun 2016 08:18:20 GMT

←Older revision		Revision as of 08:18, 1 June 2016
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SDOS_MOUSE SDOS_MOUSE]] Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors.		[[http://www.uniprot.org/uniprot/SDOS_MOUSE SDOS_MOUSE]] Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4(cyto)) in focal contacts, interacts with various cell adhesion adaptor proteins to control cell signaling. We determined the X-ray crystal structure of syndesmos; it is composed of seven alpha-helices and seven beta-strands. Although syndesmos has a molecular topology similar to that of nudix hydrolase proteins, the structure of the nudix motif differs from that of X29. The dimeric interface of syndesmos is composed of alpha-helix 4, 7 and beta-strand 2, 7, which primarily form hydrophobic interactions. The binding interaction between syndesmos and syn4(cyto) was characterized as a low-affinity interaction (Kd = 62 muM) by surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR). The NMR resonances of Lys (177, 178, 179), Gly182, and Ser183 in the C1 region and Lys193 and Lys194 in the V region of syndecan-4 are perturbed upon syndesmos binding. Our results provide structural insight into the molecular function of syndesmos in the regulation of cell signaling via binding to syndecan-4.
		+
		+	Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan.,Kim H, Yoo J, Lee I, Kang YJ, Cho HS, Lee W Biochem Biophys Res Commun. 2015 Aug 7;463(4):762-7. doi:, 10.1016/j.bbrc.2015.06.010. Epub 2015 Jun 19. PMID:26100207<ref>PMID:26100207</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4zg0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:39, 12 May 2016

OCA — Thu, 12 May 2016 18:39:09 GMT

←Older revision		Revision as of 18:39, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4zg0 ~~is ON HOLD until Apr 22 2017~~	+	==Crystal structure of Mouse Syndesmos protein==
-		+	<StructureSection load='4zg0' size='340' side='right' caption='[[4zg0]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~Authors~~: ~~Lee, I~~., ~~Kim, H~~., ~~Yoo, J~~., ~~Cho, H~~., ~~Lee, W~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4zg0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZG0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZG0 FirstGlance]. <br>
-	~~Description~~: ~~Mouse Syndesmos~~ protein	+	</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=4zg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zg0 OCA], [http://pdbe.org/4zg0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zg0 RCSB], [http://www.ebi.ac.uk/pdbsum/4zg0 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SDOS_MOUSE SDOS_MOUSE]] Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cho, H]]
	[[Category: Kim, H]]		[[Category: Kim, H]]
	[[Category: Lee, I]]		[[Category: Lee, I]]
	[[Category: Lee, W]]		[[Category: Lee, W]]
-	[[Category: Cho, H]]
	[[Category: Yoo, J]]		[[Category: Yoo, J]]
		+	[[Category: Cytoplasmic protein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nudix hydrolase]]
		+	[[Category: Syndecan-4 cytoplasmic domain interactor]]

OCA at 00:00, 1 December 2015

OCA — Tue, 01 Dec 2015 00:00:34 GMT

←Older revision		Revision as of 00:00, 1 December 2015
Line 7:		Line 7:
	Description: Mouse Syndesmos protein		Description: Mouse Syndesmos protein
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lee, W]]
-	[[Category: Cho, H]]
	[[Category: Kim, H]]		[[Category: Kim, H]]
	[[Category: Lee, I]]		[[Category: Lee, I]]
		+	[[Category: Lee, W]]
		+	[[Category: Cho, H]]
	[[Category: Yoo, J]]		[[Category: Yoo, J]]

OCA: Protected "4zg0" [edit=sysop:move=sysop]

OCA — Thu, 30 Apr 2015 10:19:43 GMT

Protected "4zg0" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:19, 30 April 2015

OCA: New page: '''Unreleased structure''' The entry 4zg0 is ON HOLD until Apr 22 2017 Authors: Lee, I., Kim, H., Yoo, J., Cho, H., Lee, W. Description: Mouse Syndesmos protein [[Category: Unreleased ...

OCA — Thu, 30 Apr 2015 10:19:41 GMT

New page: '''Unreleased structure''' The entry 4zg0 is ON HOLD until Apr 22 2017 Authors: Lee, I., Kim, H., Yoo, J., Cho, H., Lee, W. Description: Mouse Syndesmos protein [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 4zg0 is ON HOLD until Apr 22 2017

Authors: Lee, I., Kim, H., Yoo, J., Cho, H., Lee, W.

Description: Mouse Syndesmos protein
[[Category: Unreleased Structures]]
[[Category: Lee, W]]
[[Category: Cho, H]]
[[Category: Kim, H]]
[[Category: Lee, I]]
[[Category: Yoo, J]]