8b2l: Difference between revisions
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New page: '''Unreleased structure''' The entry 8b2l is ON HOLD Authors: Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Buerger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.... |
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==Cryo-EM structure of the plant 80S ribosome== | |||
<StructureSection load='8b2l' size='340' side='right'caption='[[8b2l]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8b2l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8B2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B2L 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]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8N:(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic+acid'>B8N</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=UY1:(1S)-1,4-anhydro-1-[(5S)-2,6-dioxo-1,2,5,6-tetrahydropyrimidin-5-yl]-2-O-methyl-5-O-phosphono-D-ribitol'>UY1</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=8b2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2l OCA], [https://pdbe.org/8b2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2l RCSB], [https://www.ebi.ac.uk/pdbsum/8b2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2l ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A1S4DQ51_TOBAC A0A1S4DQ51_TOBAC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 A. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing. | |||
Structure of the actively translating plant 80S ribosome at 2.2 A resolution.,Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R Nat Plants. 2023 Jun;9(6):987-1000. doi: 10.1038/s41477-023-01407-y. Epub 2023 , May 8. PMID:37156858<ref>PMID:37156858</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[ | </div> | ||
[[Category: | <div class="pdbe-citations 8b2l" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Bock | ==See Also== | ||
[[Category: Buerger | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
[[Category: Kleinau | == References == | ||
[[Category: Loerke | <references/> | ||
[[Category: Mielke | __TOC__ | ||
[[Category: Schmidt | </StructureSection> | ||
[[Category: Smirnova | [[Category: Large Structures]] | ||
[[Category: Spahn | [[Category: Nicotiana tabacum]] | ||
[[Category: | [[Category: Bock R]] | ||
[[Category: Buerger J]] | |||
[[Category: Kleinau G]] | |||
[[Category: Loerke J]] | |||
[[Category: Meyer EH]] | |||
[[Category: Mielke T]] | |||
[[Category: Scheerer P]] | |||
[[Category: Schmidt A]] | |||
[[Category: Smirnova J]] | |||
[[Category: Spahn CMT]] | |||
[[Category: Zoschke R]] | |||
Latest revision as of 05:38, 24 June 2026
Cryo-EM structure of the plant 80S ribosome
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