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| | ==Structure of the translating mammalian ribosome-Sec61 complex== | | ==Structure of the translating mammalian ribosome-Sec61 complex== |
| - | <SX load='3j7r' size='340' side='right' viewer='molstar' caption='[[3j7r]], [[Resolution|resolution]] 3.90Å' scene=''> | + | <SX load='3j7r' size='340' side='right' viewer='molstar' caption='[[3j7r]], [[Resolution|resolution]] 3.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3j7r]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w26 4w26], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w27 4w27], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w28 4w28], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx0 1vx0], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx1 1vx1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx2 1vx2] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j73 3j73]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J7R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3j7r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w26 4w26], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w27 4w27], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w28 4w28], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx0 1vx0], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx1 1vx1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx2 1vx2] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j73 3j73]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J7R FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.9Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j7o|3j7o]], [[3j7p|3j7p]], [[3j7q|3j7q]]</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=3j7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7r OCA], [https://pdbe.org/3j7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j7r RCSB], [https://www.ebi.ac.uk/pdbsum/3j7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7r 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=3j7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7r OCA], [http://pdbe.org/3j7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j7r RCSB], [http://www.ebi.ac.uk/pdbsum/3j7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RL40_PIG RL40_PIG]] 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, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. 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). 60S ribosomal protein L40: component of the 60S subunit of the ribosome (By similarity). [[http://www.uniprot.org/uniprot/B6V8C8_PIG B6V8C8_PIG]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122] [[http://www.uniprot.org/uniprot/RS18_PIG RS18_PIG]] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL11_PIG RL11_PIG]] Binds to 5S ribosomal RNA (By similarity). Required for rRNA maturation and formation of the 60S ribosomal subunits. Promotes nucleolar location of PML (By similarity). [[http://www.uniprot.org/uniprot/RSSA_PIG RSSA_PIG]] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Also acts as a receptor for several other ligands, including the pathogenic prion protein, viruses, and bacteria. Acts as a PPP1R16B-dependent substrate of PPP1CA (By similarity).<ref>PMID:15790424</ref> | + | [https://www.uniprot.org/uniprot/F1SJJ5_PIG F1SJJ5_PIG] Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.[ARBA:ARBA00034092] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | == References == | | == References == |
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| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| | + | [[Category: Large Structures]] |
| | [[Category: Sus scrofa]] | | [[Category: Sus scrofa]] |
| - | [[Category: Fernandez, I S]] | + | [[Category: Fernandez IS]] |
| - | [[Category: Hegde, R S]] | + | [[Category: Hegde RS]] |
| - | [[Category: Scheres, S H.W]] | + | [[Category: Scheres SHW]] |
| - | [[Category: Voorhees, R M]] | + | [[Category: Voorhees RM]] |
| - | [[Category: Mammalian]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Sec61]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: Translocation]]
| + | |
