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6gz3

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tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)

6gz3, resolution 3.60Å

Structural highlights

6gz3 is a 10 chain structure with sequence from Oryctolagus cuniculus, Saccharomyces cerevisiae and Salmonella virus SP6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.6Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS5_RABIT Component of the small ribosomal subunit (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (By similarity).[UniProtKB:P46782]^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Translocation moves the tRNA2mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA2mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.,Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Burger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV Cell Rep. 2018 Dec 4;25(10):2676-2688.e7. doi: 10.1016/j.celrep.2018.11.040. PMID:30517857^[5]

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

References

↑ Lomakin IB, Steitz TA. The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature. 2013 Jul 21. doi: 10.1038/nature12355. PMID:23873042 doi:10.1038/nature12355
↑ 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:http://dx.doi.org/10.1016/j.molcel.2014.12.016
↑ 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:http://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:http://dx.doi.org/10.1016/j.celrep.2018.11.040
↑ 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:http://dx.doi.org/10.1016/j.celrep.2018.11.040

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6gz3"

@@ Line 3: / Line 3: @@
 <SX load='6gz3' size='340' side='right' viewer='molstar' caption='[[6gz3]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6gz3]] is a 86 chain structure with sequence from [https://en.wikipedia.org/wiki/European_rabbit European rabbit], [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GZ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6gz3]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Salmonella_virus_SP6 Salmonella virus SP6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GZ3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDE:{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM'>DDE</scene></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=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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=6gz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gz3 OCA], [https://pdbe.org/6gz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gz3 RCSB], [https://www.ebi.ac.uk/pdbsum/6gz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gz3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[https://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]
+[https://www.uniprot.org/uniprot/RS5_RABIT RS5_RABIT] Component of the small ribosomal subunit (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit (PubMed:23873042, PubMed:25601755, PubMed:27863242, PubMed:30517857). During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (By similarity).[UniProtKB:P46782]<ref>PMID:23873042</ref> <ref>PMID:25601755</ref> <ref>PMID:27863242</ref> <ref>PMID:30517857</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </SX>
-[[Category: European rabbit]]
 [[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Blanchard, S C]]
+[[Category: Salmonella virus SP6]]
-[[Category: Budkevich, T V]]
+[[Category: Blanchard SC]]
-[[Category: Buerger, J]]
+[[Category: Budkevich TV]]
-[[Category: Dabrowski, M]]
+[[Category: Buerger J]]
-[[Category: Flis, J]]
+[[Category: Dabrowski M]]
-[[Category: Hilal, T]]
+[[Category: Flis J]]
-[[Category: Holm, M]]
+[[Category: Hilal T]]
-[[Category: Loerke, J]]
+[[Category: Holm M]]
-[[Category: Mielke, T]]
+[[Category: Loerke J]]
-[[Category: Rundlet, E J]]
+[[Category: Mielke T]]
-[[Category: Spahn, C M.T]]
+[[Category: Rundlet EJ]]
-[[Category: Eef2]]
+[[Category: Spahn CMT]]
-[[Category: Head swivel]]
-[[Category: Ribosome]]
-[[Category: Rotation]]
-[[Category: Translocation rabbit ribosome]]

6gz3

From Proteopedia

Current revision

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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