6yal: Difference between revisions

Latest revision as of 18:43, 8 September 2026

Mammalian 48S late-stage initiation complex with beta-globin mRNA

Structural highlights

6yal 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:	C4J, GNP, MG, T6A
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS32_RABIT Component of the small ribosomal subunit (PubMed:24995983, PubMed:27863242). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:24995983, PubMed:27863242). Interacts with the beta subunit of protein kinase CKII and stimulates phosphorylation of DNA topoisomerase II alpha by CKII (By similarity).[UniProtKB:P62945]^[1] ^[2]

Publication Abstract from PubMed

In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, beta-globin and histone 4, at overall resolution of 3 and 3.5 A, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.

Structural Insights into the Mammalian Late-Stage Initiation Complexes.,Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y Cell Rep. 2020 Apr 7;31(1):107497. doi: 10.1016/j.celrep.2020.03.061. PMID:32268096^[3]

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

References

↑ Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM. Regulation of the Mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell. 2014 Jul 3;158(1):121-31. doi: 10.1016/j.cell.2014.04.044. PMID:24995983 doi:https://dx.doi.org/10.1016/j.cell.2014.04.044
↑ 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
↑ Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep. 2020 Apr 7;31(1):107497. doi: 10.1016/j.celrep.2020.03.061. PMID:32268096 doi:https://dx.doi.org/10.1016/j.celrep.2020.03.061

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OCA

[1] Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM. Regulation of the Mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell. 2014 Jul 3;158(1):121-31. doi: 10.1016/j.cell.2014.04.044. PMID:24995983 doi:https://dx.doi.org/10.1016/j.cell.2014.04.044

[2] 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

[3] Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep. 2020 Apr 7;31(1):107497. doi: 10.1016/j.celrep.2020.03.061. PMID:32268096 doi:https://dx.doi.org/10.1016/j.celrep.2020.03.061

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[3]

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[6yal]] 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=6YAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YAL 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=C4J:(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol'>C4J</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C4J:(2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{S})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic+acid'>C4J</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</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=6yal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yal OCA], [https://pdbe.org/6yal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yal RCSB], [https://www.ebi.ac.uk/pdbsum/6yal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yal ProSAT]</span></td></tr>
 </table>

6yal: Difference between revisions

Latest revision as of 18:43, 8 September 2026

Mammalian 48S late-stage initiation complex with beta-globin mRNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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