5gvd: Difference between revisions

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'''Unreleased structure'''


The entry 5gvd is ON HOLD  until Paper Publication
==Human TDRD3 DUF1767-OB domains==
<StructureSection load='5gvd' size='340' side='right'caption='[[5gvd]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gvd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GVD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.623&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5gvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gvd OCA], [https://pdbe.org/5gvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gvd RCSB], [https://www.ebi.ac.uk/pdbsum/5gvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gvd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TDRD3_HUMAN TDRD3_HUMAN] Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.<ref>PMID:18632687</ref> <ref>PMID:15955813</ref> <ref>PMID:21172665</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Topoisomerase IIIbeta (TOP3beta) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3beta co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3beta to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3beta, the DUF1767-OB-fold domains of TDRD3 and their complex at 3.44 A, 1.62 A and 3.6 A resolutions, respectively. The toroidal-shaped catalytic domain of TOP3beta binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3beta. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIalpha (TOP3alpha)-RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3beta to avoid the non-cognate interaction with TOP3alpha.


Authors:  
Structural basis of the interaction between Topoisomerase IIIbeta and the TDRD3 auxiliary factor.,Goto-Ito S, Yamagata A, Takahashi TS, Sato Y, Fukai S Sci Rep. 2017 Feb 8;7:42123. doi: 10.1038/srep42123. PMID:28176834<ref>PMID:28176834</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5gvd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Fukai S]]
[[Category: Goto-Ito S]]
[[Category: Sato Y]]
[[Category: Takahashi TS]]
[[Category: Yamagata A]]
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