4v8t: Difference between revisions

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 <SX load='4v8t' size='340' side='right' viewer='molstar' caption='[[4v8t]], [[Resolution|resolution]] 8.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v8t]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b6a 4b6a] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b6b 4b6b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V8T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v8t]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b6a 4b6a] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b6b 4b6b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V8T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 8.1&#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=ZN:ZINC+ION'>ZN</scene></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=4v8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8t OCA], [http://pdbe.org/4v8t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v8t RCSB], [http://www.ebi.ac.uk/pdbsum/4v8t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v8t ProSAT]</span></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=4v8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8t OCA], [https://pdbe.org/4v8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v8t RCSB], [https://www.ebi.ac.uk/pdbsum/4v8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v8t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/RL11B_YEAST RL11B_YEAST]] Binds to 5S ribosomal RNA. [[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/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref>  [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/RLA0_YEAST RLA0_YEAST]] Ribosomal protein P0 is the functional equivalent of E.coli protein L10.
+[https://www.uniprot.org/uniprot/RL2A_YEAST RL2A_YEAST]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
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 __TOC__
 </SX>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Ban, N]]
+[[Category: Ban N]]
-[[Category: Boehringer, D]]
+[[Category: Boehringer D]]
-[[Category: Greber, B J]]
+[[Category: Greber BJ]]
-[[Category: Montellese, C]]
+[[Category: Montellese C]]
-[[Category: Large ribosomal subunit]]
-[[Category: Ribosome]]
-[[Category: Ribosome biogenesis]]
-[[Category: Ribosome maturation factor]]