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| | <SX load='3j7o' size='340' side='right' viewer='molstar' caption='[[3j7o]], [[Resolution|resolution]] 3.50Å' scene=''> | | <SX load='3j7o' size='340' side='right' viewer='molstar' caption='[[3j7o]], [[Resolution|resolution]] 3.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3j7o]] is a 45 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=4w1z 4w1z], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w20 4w20], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vww 1vww], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwx 1vwx] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j71 3j71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J7O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3j7o]] is a 45 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=4w1z 4w1z], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w20 4w20], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vww 1vww], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwx 1vwx] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j71 3j71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J7O FirstGlance]. <br> |
| | </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> | | </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">[[3j7p|3j7p]], [[3j7q|3j7q]], [[3j7r|3j7r]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3j7p|3j7p]], [[3j7q|3j7q]], [[3j7r|3j7r]]</div></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3j7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7o OCA], [http://pdbe.org/3j7o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j7o RCSB], [http://www.ebi.ac.uk/pdbsum/3j7o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7o 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=3j7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7o OCA], [https://pdbe.org/3j7o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j7o RCSB], [https://www.ebi.ac.uk/pdbsum/3j7o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7o ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/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). | + | [[https://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). [[https://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). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Structural highlights
Function
[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). [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).
Publication Abstract from PubMed
Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 A resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.,Voorhees RM, Fernandez IS, Scheres SH, Hegde RS Cell. 2014 Jun 19;157(7):1632-43. doi: 10.1016/j.cell.2014.05.024. Epub 2014 Jun , 12. PMID:24930395[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Voorhees RM, Fernandez IS, Scheres SH, Hegde RS. Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution. Cell. 2014 Jun 19;157(7):1632-43. doi: 10.1016/j.cell.2014.05.024. Epub 2014 Jun , 12. PMID:24930395 doi:http://dx.doi.org/10.1016/j.cell.2014.05.024
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