View source for 9qdq


==Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA==
<StructureSection load='9qdq' size='340' side='right'caption='[[9qdq]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9qdq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QDQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6&#8491;</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=9qdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qdq OCA], [https://pdbe.org/9qdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qdq RCSB], [https://www.ebi.ac.uk/pdbsum/9qdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qdq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NMD4_YEAST NMD4_YEAST] Involved in nonsense-mediated decay of mRNAs containing premature stop codons.<ref>PMID:7883168</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Upf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In Saccharomyces cerevisiae, Upf1 exists in two distinct complexes with factors that mediate NMD activation or 5'-3' mRNA degradation. We combined endogenous purifications and biochemical reconstitutions of yeast Upf1 complexes with structural analyses and biochemical assays to elucidate the molecular mechanisms driving the organization of the Upf1-5'-3' and Upf1-2-3 complexes. We show that yeast Upf1 is in a constitutive complex, whereby its CH, RecA, and C-terminal domains interact with the mRNA decapping factor Dcp2, NMD-associated proteins Nmd4 and Ebs1, and the 5'-3' exoribonuclease Xrn1, respectively. Together, the interacting surfaces and closed conformation of Upf1 in the Upf1-5'-3' complex sterically obstruct the binding of Upf2-3. Our work points to a major restructuring upon recruitment of these factors during NMD and provides insights into evolutionary divergence amongst species.

Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast.,Iermak I, Wilson Eisele NR, Kurscheidt K, Loukeri MJ, Basquin J, Bonneau F, Langer LM, Keidel A, Conti E Cell Rep. 2025 Oct 10;44(10):116415. doi: 10.1016/j.celrep.2025.116415. PMID:41076630<ref>PMID:41076630</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9qdq" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Basquin J]]
[[Category: Bonneau F]]
[[Category: Conti E]]
[[Category: Iermak I]]
[[Category: Keidel A]]
[[Category: Kurscheidt K]]
[[Category: Langer LM]]
[[Category: Loukeri MJ]]
[[Category: Wilson Eisele NR]]