9q2m: Difference between revisions

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'''Unreleased structure'''


The entry 9q2m is ON HOLD
==Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site Ala-tRNA on NediV ORF==
<StructureSection load='9q2m' size='340' side='right'caption='[[9q2m]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9q2m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9Q2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Q2M 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]] 3.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDE:{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM'>DDE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9q2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9q2m OCA], [https://pdbe.org/9q2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9q2m RCSB], [https://www.ebi.ac.uk/pdbsum/9q2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9q2m ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL19_RABIT RL19_RABIT] Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.[UniProtKB:P84098]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high-resolution structures of 80S ribosome complexes with the NediV IRES in various functional states, including binary complexes, aminoacyl-transfer RNA (tRNA)-bound complexes, and complexes with elongation factor eEF2. In binary complexes, the NediV IRES primarily occupies the ribosomal P site, exhibiting conformational flexibility and engaging the ribosome at multiple interaction sites. Upon translocation, the IRES undergoes structural rearrangements, including destabilization of its PKI domain, facilitating the transition to canonical elongation. Crucially, we captured an eEF2-bound complex, along with an eEF1A-bound failed decoding complex featuring a mismatched tRNA, the latter representing the first instance of a canonical elongation complex visualized in the presence of a natural, hydrolysable nucleotide and without the addition of any trapping agents. These findings provide a comprehensive structural overview of IGR IRES-mediated translation initiation and its transition to elongation, revealing key mechanistic details of viral translation and proofreading.


Authors: De, S., Altomare, C.G., Abaeva, I.S., Dadhwal, P., Garg, P., Acosta-Reyes, F., Brown, Z.P., Pestova, T.V., Hellen, C.U.T., Frank, J.
Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation.,De S, Altomare CG, Abaeva IS, Dadhwal P, Garg P, Acosta-Reyes F, Brown ZP, Pestova TV, Hellen CUT, Frank J Nucleic Acids Res. 2026 May 20;54(10):gkag510. doi: 10.1093/nar/gkag510. PMID:42240621<ref>PMID:42240621</ref>


Description: Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site Ala-tRNA on NediV ORF
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Brown, Z.P]]
<div class="pdbe-citations 9q2m" style="background-color:#fffaf0;"></div>
[[Category: Dadhwal, P]]
== References ==
[[Category: Altomare, C.G]]
<references/>
[[Category: Frank, J]]
__TOC__
[[Category: De, S]]
</StructureSection>
[[Category: Abaeva, I.S]]
[[Category: Large Structures]]
[[Category: Pestova, T.V]]
[[Category: Oryctolagus cuniculus]]
[[Category: Garg, P]]
[[Category: Abaeva IS]]
[[Category: Acosta-Reyes, F]]
[[Category: Acosta-Reyes F]]
[[Category: Hellen, C.U.T]]
[[Category: Altomare CG]]
[[Category: Brown ZP]]
[[Category: Dadhwal P]]
[[Category: De S]]
[[Category: Frank J]]
[[Category: Garg P]]
[[Category: Hellen CUT]]
[[Category: Pestova TV]]
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