5t6r: Difference between revisions

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 <SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t6r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 4.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t62|5t62]]</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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [https://pdbe.org/5t6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [https://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
-<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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/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).
+[https://www.uniprot.org/uniprot/RL7A_YEAST RL7A_YEAST]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.
-Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.,Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW EMBO J. 2017 Feb 8. pii: e201696012. doi: 10.15252/embj.201696012. PMID:28179369<ref>PMID:28179369</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5t6r" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribosome 3D structures|Ribosome 3D structures]]
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Frank, J]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Johnson, A W]]
+[[Category: Frank J]]
-[[Category: Malyutin, A G]]
+[[Category: Johnson AW]]
-[[Category: Musalgaonkar, S]]
+[[Category: Malyutin AG]]
-[[Category: Patchett, S]]
+[[Category: Musalgaonkar S]]
-[[Category: Cryo-em]]
+[[Category: Patchett S]]
-[[Category: Lsg1]]
-[[Category: Nmd3]]
-[[Category: Ribosome]]
-[[Category: Ribosome biogenesis]]
-[[Category: Tif6]]