9q2p: Difference between revisions

Latest revision as of 07:15, 17 June 2026

Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF

Structural highlights

9q2p is a 10 chain structure with sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3Å
Ligands:	GTP, MG, SEP, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL8_RABIT Component of the large ribosomal subunit (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857).^[1] ^[2] ^[3] ^[4]

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.

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^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM. Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES. Mol Cell. 2015 Feb 5;57(3):422-432. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 , Jan 15. PMID:25601755 doi:https://dx.doi.org/10.1016/j.molcel.2014.12.016
↑ Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V. Structural basis for stop codon recognition in eukaryotes. Nature. 2015 Aug 27;524(7566):493-6. doi: 10.1038/nature14896. Epub 2015 Aug 5. PMID:26245381 doi:https://dx.doi.org/10.1038/nature14896
↑ Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Cell. 2016 Nov 17;167(5):1229-1240.e15. doi: 10.1016/j.cell.2016.10.046. PMID:27863242 doi:https://dx.doi.org/10.1016/j.cell.2016.10.046
↑ Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Burger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep. 2018 Dec 4;25(10):2676-2688.e7. doi: 10.1016/j.celrep.2018.11.040. PMID:30517857 doi:https://dx.doi.org/10.1016/j.celrep.2018.11.040
↑ De S, Altomare CG, Abaeva IS, Dadhwal P, Garg P, Acosta-Reyes F, Brown ZP, Pestova TV, Hellen CUT, Frank J. Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation. Nucleic Acids Res. 2026 May 20;54(10):gkag510. doi: 10.1093/nar/gkag510. PMID:42240621 doi:https://dx.doi.org/10.1093/nar/gkag510

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM. Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES. Mol Cell. 2015 Feb 5;57(3):422-432. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 , Jan 15. PMID:25601755 doi:https://dx.doi.org/10.1016/j.molcel.2014.12.016

[2] Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V. Structural basis for stop codon recognition in eukaryotes. Nature. 2015 Aug 27;524(7566):493-6. doi: 10.1038/nature14896. Epub 2015 Aug 5. PMID:26245381 doi:https://dx.doi.org/10.1038/nature14896

[3] Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Cell. 2016 Nov 17;167(5):1229-1240.e15. doi: 10.1016/j.cell.2016.10.046. PMID:27863242 doi:https://dx.doi.org/10.1016/j.cell.2016.10.046

[4] Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Burger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep. 2018 Dec 4;25(10):2676-2688.e7. doi: 10.1016/j.celrep.2018.11.040. PMID:30517857 doi:https://dx.doi.org/10.1016/j.celrep.2018.11.040

[5] De S, Altomare CG, Abaeva IS, Dadhwal P, Garg P, Acosta-Reyes F, Brown ZP, Pestova TV, Hellen CUT, Frank J. Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation. Nucleic Acids Res. 2026 May 20;54(10):gkag510. doi: 10.1093/nar/gkag510. PMID:42240621 doi:https://dx.doi.org/10.1093/nar/gkag510

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9q2p is ON HOLD
+==Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF==
+<StructureSection load='9q2p' size='340' side='right'caption='[[9q2p]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9q2p]] 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=9Q2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Q2P 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=9q2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9q2p OCA], [https://pdbe.org/9q2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9q2p RCSB], [https://www.ebi.ac.uk/pdbsum/9q2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9q2p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL8_RABIT RL8_RABIT] Component of the large ribosomal subunit (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857).<ref>PMID:25601755</ref> <ref>PMID:26245381</ref> <ref>PMID:27863242</ref> <ref>PMID:30517857</ref>
+<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 eEF1A, A*/T Ala-tRNA, 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: De, S]]
+<div class="pdbe-citations 9q2p" style="background-color:#fffaf0;"></div>
-[[Category: Altomare, C.G]]
+== References ==
-[[Category: Garg, P]]
+<references/>
-[[Category: Pestova, T.V]]
+__TOC__
-[[Category: Abaeva, I.S]]
+</StructureSection>
-[[Category: Frank, J]]
+[[Category: Large Structures]]
-[[Category: Brown, Z.P]]
+[[Category: Oryctolagus cuniculus]]
-[[Category: Hellen, C.U.T]]
+[[Category: Abaeva IS]]
-[[Category: Acosta-Reyes, F]]
+[[Category: Acosta-Reyes F]]
-[[Category: Dadhwal, P]]
+[[Category: Altomare CG]]
+[[Category: Brown ZP]]
+[[Category: Dadhwal P]]
+[[Category: De S]]
+[[Category: Frank J]]
+[[Category: Garg P]]
+[[Category: Hellen CUT]]
+[[Category: Pestova TV]]

9q2p: Difference between revisions

Latest revision as of 07:15, 17 June 2026

Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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