6tqa - Revision history

OCA at 13:07, 24 January 2024

OCA — Wed, 24 Jan 2024 13:07:18 GMT

←Older revision		Revision as of 13:07, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tqa' size='340' side='right'caption='[[6tqa]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6tqa' size='340' side='right'caption='[[6tqa]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tqa]] is a 8 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=6TQA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tqa]] is a 8 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=6TQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TQA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~Rc3h1~~, ~~Gm551, Kiaa2025 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6tqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqa OCA], [https://pdbe.org/6tqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tqa RCSB], [https://www.ebi.ac.uk/pdbsum/6tqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqa ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27]~~ </~~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=6tqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqa OCA], [~~http~~://pdbe.org/6tqa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tqa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tqa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqa ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RC3H1_MOUSE RC3H1_MOUSE]] Post-transcriptional repressor of mRNAs containing a conserved stem loop motif, called constitutive decay element (CDE), which is often located in the 3'-UTR, as in HMGXB3, ICOS, IER3, NFKBID, NFKBIZ, PPP1R10, TNF and in many more mRNAs (PubMed:23663784). Binds to CDE and promotes mRNA deadenylation and degradation. This process does not involve miRNAs. In follicular helper T (Tfh) cells, represses of ICOS and TNFRSF4/Ox40 expression, thus preventing spontaneous Tfh cell differentiation, germinal center B-cell differentiation in the absence of immunization and autoimmunity. In resting or LPS-stimulated macrophages, controls inflammation by suppressing TNF expression. Also recognizes CDE in its own mRNA and in that of paralogous RC3H2, possibly leading to feedback loop regulation.<ref>PMID:15917799</ref> <ref>PMID:18172933</ref> <ref>PMID:20412057</ref> <ref>PMID:20639877</ref> <ref>PMID:23663784</ref> <ref>PMID:23583643</ref> <ref>PMID:23583642</ref>	+	[https://www.uniprot.org/uniprot/RC3H1_MOUSE RC3H1_MOUSE] Post-transcriptional repressor of mRNAs containing a conserved stem loop motif, called constitutive decay element (CDE), which is often located in the 3'-UTR, as in HMGXB3, ICOS, IER3, NFKBID, NFKBIZ, PPP1R10, TNF and in many more mRNAs (PubMed:23663784). Binds to CDE and promotes mRNA deadenylation and degradation. This process does not involve miRNAs. In follicular helper T (Tfh) cells, represses of ICOS and TNFRSF4/Ox40 expression, thus preventing spontaneous Tfh cell differentiation, germinal center B-cell differentiation in the absence of immunization and autoimmunity. In resting or LPS-stimulated macrophages, controls inflammation by suppressing TNF expression. Also recognizes CDE in its own mRNA and in that of paralogous RC3H2, possibly leading to feedback loop regulation.<ref>PMID:15917799</ref> <ref>PMID:18172933</ref> <ref>PMID:20412057</ref> <ref>PMID:20639877</ref> <ref>PMID:23663784</ref> <ref>PMID:23583643</ref> <ref>PMID:23583642</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: RING-type E3 ubiquitin transferase~~]]	+	[[Category: Binas O]]
-	[[Category: Binas, O]]	+	[[Category: Braun J]]
-	[[Category: Braun, J]]	+	[[Category: Davydova E]]
-	[[Category: Davydova, E]]	+	[[Category: Janowski R]]
-	[[Category: Janowski, R]]	+	[[Category: Niessing D]]
-	[[Category: Niessing, D]]	+	[[Category: Peter SA]]
-	[[Category: Peter~~, S A~~]]	+	[[Category: Schlundt A]]
-	[[Category: Schlundt, A]]	+	[[Category: Schwalbe H]]
-	[[Category: Schwalbe, H]]	+	[[Category: Tants J-N]]
-	[[Category: Tants, J N]]	+	[[Category: Weigand JE]]
-	[[Category: Weigand~~, J E]]~~	+
-	~~[[Category: Cde2]]~~	+
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Roq domain]]~~	+
-	~~[[Category: Roquin~~]]	+

OCA at 10:40, 17 June 2020

OCA — Wed, 17 Jun 2020 10:40:39 GMT

←Older revision		Revision as of 10:40, 17 June 2020
Line 1:		Line 1:

	==X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 SL RNA motif==		==X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 SL RNA motif==
-	<StructureSection load='6tqa' size='340' side='right'caption='[[6tqa]]' scene=''>	+	<StructureSection load='6tqa' size='340' side='right'caption='[[6tqa]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tqa]] is a 8 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=6TQA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQA FirstGlance]. <br>
-	</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=6tqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqa OCA], [http://pdbe.org/6tqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqa RCSB], [http://www.ebi.ac.uk/pdbsum/6tqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqa ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rc3h1, Gm551, Kiaa2025 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6tqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqa OCA], [http://pdbe.org/6tqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqa RCSB], [http://www.ebi.ac.uk/pdbsum/6tqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RC3H1_MOUSE RC3H1_MOUSE]] Post-transcriptional repressor of mRNAs containing a conserved stem loop motif, called constitutive decay element (CDE), which is often located in the 3'-UTR, as in HMGXB3, ICOS, IER3, NFKBID, NFKBIZ, PPP1R10, TNF and in many more mRNAs (PubMed:23663784). Binds to CDE and promotes mRNA deadenylation and degradation. This process does not involve miRNAs. In follicular helper T (Tfh) cells, represses of ICOS and TNFRSF4/Ox40 expression, thus preventing spontaneous Tfh cell differentiation, germinal center B-cell differentiation in the absence of immunization and autoimmunity. In resting or LPS-stimulated macrophages, controls inflammation by suppressing TNF expression. Also recognizes CDE in its own mRNA and in that of paralogous RC3H2, possibly leading to feedback loop regulation.<ref>PMID:15917799</ref> <ref>PMID:18172933</ref> <ref>PMID:20412057</ref> <ref>PMID:20639877</ref> <ref>PMID:23663784</ref> <ref>PMID:23583643</ref> <ref>PMID:23583642</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Adenylate/uridylate-rich elements (AREs) are the most common cis-regulatory elements in the 3'-untranslated region (UTR) of mRNAs, where they fine-tune turnover by mediating mRNA decay. They increase plasticity and efficacy of mRNA regulation and are recognized by several ARE-specific RNA-binding proteins (RBPs). Typically, AREs are short linear motifs with a high content of complementary A and U nucleotides and often occur in multiple copies. Although thermodynamically rather unstable, the high AU-content might enable transient secondary structure formation and modify mRNA regulation by RBPs. We have recently suggested that the immunoregulatory RBP Roquin recognizes folded AREs as constitutive decay elements (CDEs), resulting in shape-specific ARE-mediated mRNA degradation. However, the structural evidence for a CDE-like recognition of AREs by Roquin is still lacking. We here present structures of CDE-like folded AREs, both in their free and protein-bound form. Moreover, the AREs in the UCP3 3'-UTR are additionally bound by the canonical ARE-binding protein AUF1 in their linear form, adopting an alternative binding-interface compared to the recognition of their CDE structure by Roquin. Strikingly, our findings thus suggest that AREs can be recognized in multiple ways, allowing control over mRNA regulation by adapting distinct conformational states, thus providing differential accessibility to regulatory RBPs.
		+
		+	Structural basis for the recognition of transiently structured AU-rich elements by Roquin.,Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A Nucleic Acids Res. 2020 Jun 3. pii: 5850806. doi: 10.1093/nar/gkaa465. PMID:32491174<ref>PMID:32491174</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tqa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Binas O]]	+	[[Category: Lk3 transgenic mice]]
-	[[Category: Braun J]]	+	[[Category: RING-type E3 ubiquitin transferase]]
-	[[Category: Davydova E]]	+	[[Category: Binas, O]]
-	[[Category: Janowski R]]	+	[[Category: Braun, J]]
-	[[Category: Niessing D]]	+	[[Category: Davydova, E]]
-	[[Category: Peter SA]]	+	[[Category: Janowski, R]]
-	[[Category: Schlundt A]]	+	[[Category: Niessing, D]]
-	[[Category: Schwalbe H]]	+	[[Category: Peter, S A]]
-	[[Category: Tants J-N]]	+	[[Category: Schlundt, A]]
-	[[Category: Weigand JE]]	+	[[Category: Schwalbe, H]]
		+	[[Category: Tants, J N]]
		+	[[Category: Weigand, J E]]
		+	[[Category: Cde2]]
		+	[[Category: Rna binding]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Roq domain]]
		+	[[Category: Roquin]]

OCA at 06:59, 27 May 2020

OCA — Wed, 27 May 2020 06:59:12 GMT

←Older revision		Revision as of 06:59, 27 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tqa is ~~ON HOLD until Paper Publication~~	+	==X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 SL RNA motif==
-		+	<StructureSection load='6tqa' size='340' side='right'caption='[[6tqa]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQA FirstGlance]. <br>
-	~~Description~~:	+	</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=6tqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqa OCA], [http://pdbe.org/6tqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqa RCSB], [http://www.ebi.ac.uk/pdbsum/6tqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Binas O]]
		+	[[Category: Braun J]]
		+	[[Category: Davydova E]]
		+	[[Category: Janowski R]]
		+	[[Category: Niessing D]]
		+	[[Category: Peter SA]]
		+	[[Category: Schlundt A]]
		+	[[Category: Schwalbe H]]
		+	[[Category: Tants J-N]]
		+	[[Category: Weigand JE]]

OCA: Protected "6tqa" [edit=sysop:move=sysop]

OCA — Wed, 25 Dec 2019 07:21:53 GMT

Protected "6tqa" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:21, 25 December 2019

OCA: New page: '''Unreleased structure''' The entry 6tqa is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Dec 2019 07:21:51 GMT

New page: '''Unreleased structure''' The entry 6tqa is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tqa is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]