5apo

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==Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1==
==Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1==
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<StructureSection load='5apo' size='340' side='right' caption='[[5apo]], [[Resolution|resolution]] 3.41&Aring;' scene=''>
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<SX load='5apo' size='340' side='right' viewer='molstar' caption='[[5apo]], [[Resolution|resolution]] 3.41&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5apo]] is a 47 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5APO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5APO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5apo]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5APO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5APO FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.41&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>, <scene name='pdbligand=Y5P:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,4-DIHYDROPYRIMIDINE'>Y5P</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene>, <scene name='pdbligand=Y5P:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,4-DIHYDROPYRIMIDINE'>Y5P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5apn|5apn]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5apo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5apo OCA], [https://pdbe.org/5apo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5apo RCSB], [https://www.ebi.ac.uk/pdbsum/5apo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5apo ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5apo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5apo OCA], [http://pdbe.org/5apo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5apo RCSB], [http://www.ebi.ac.uk/pdbsum/5apo PDBsum]</span></td></tr>
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</table>
</table>
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{{Large structure}}
 
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/RL25_YEAST RL25_YEAST]] This protein binds to a specific region on the 26S rRNA. [[http://www.uniprot.org/uniprot/RLA0_YEAST RLA0_YEAST]] Ribosomal protein P0 is the functional equivalent of E.coli protein L10. [[http://www.uniprot.org/uniprot/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref> [[http://www.uniprot.org/uniprot/RL401_YEAST RL401_YEAST]] Ubiquitin: exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).<ref>PMID:23169626</ref> 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.<ref>PMID:23169626</ref> [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/ARX1_YEAST ARX1_YEAST]] Probable metalloprotease involved in proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Accompanies the pre-60S particles to the cytoplasm.<ref>PMID:12374754</ref> <ref>PMID:16648468</ref>
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[https://www.uniprot.org/uniprot/RL2A_YEAST RL2A_YEAST]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 A resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.
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Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.,Greber BJ, Gerhardy S, Leitner A, Leibundgut M, Salem M, Boehringer D, Leulliot N, Aebersold R, Panse VG, Ban N Cell. 2016 Jan 14;164(1-2):91-102. doi: 10.1016/j.cell.2015.11.027. Epub 2015 Dec, 17. PMID:26709046<ref>PMID:26709046</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5apo" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
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</StructureSection>
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</SX>
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[[Category: Saccharomyces cerevisiae s288c]]
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[[Category: Large Structures]]
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[[Category: Aebersold, R]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Ban, N]]
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[[Category: Aebersold R]]
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[[Category: Boehringer, D]]
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[[Category: Ban N]]
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[[Category: Gerhardy, S]]
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[[Category: Boehringer D]]
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[[Category: Greber, B J]]
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[[Category: Gerhardy S]]
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[[Category: Leibundgut, M]]
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[[Category: Greber BJ]]
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[[Category: Leitner, A]]
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[[Category: Leibundgut M]]
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[[Category: Leulliot, N]]
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[[Category: Leitner A]]
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[[Category: Panse, V G]]
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[[Category: Leulliot N]]
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[[Category: Salem, M]]
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[[Category: Panse VG]]
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[[Category: 60s ribosomal subunit]]
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[[Category: Salem M]]
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[[Category: Alb1]]
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[[Category: Arx1]]
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[[Category: Cryo-em]]
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[[Category: Eukaryotic ribosome biogenesis]]
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[[Category: Rei1]]
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[[Category: Ribosomal polypeptide exit tunnel proofreading]]
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[[Category: Ribosome]]
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[[Category: Ribosome biogenesis factor]]
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[[Category: Ribosome maturation]]
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Current revision

Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1

5apo, resolution 3.41Å

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