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3j7q

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Revision as of 18:06, 10 April 2020

Structure of the idle mammalian ribosome-Sec61 complex

3j7q, resolution 3.50Å

Structural highlights

3j7q is a 48 chain structure with sequence from Sus scrofa. This structure supersedes the now removed PDB entries 4w24, 4w25, 1vwy, 1vwz and 3j72. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3j7o, 3j7p, 3j7r
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RL34_PIG] Component of the large ribosomal subunit.^[1] [RL21_PIG] Component of the large ribosomal subunit.^[2] [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). [RL10_PIG] Component of the large ribosomal subunit. Plays a role in the formation of actively translating ribosomes. May play a role in the embryonic brain development.[UniProtKB:P27635] [RL6_PIG] Component of the large ribosomal subunit.^[3] [A0A480UVT3_PIG] Binds to the 23S rRNA.[RuleBase:RU000576]

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^[4]

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
↑ 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
↑ 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
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3j7q"

@@ Line 3: / Line 3: @@
 <SX load='3j7q' size='340' side='right' viewer='molstar' caption='[[3j7q]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3j7q]] is a 48 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=4w24 4w24], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w25 4w25], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwy 1vwy], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwz 1vwz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j72 3j72]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J7Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3j7q]] is a 48 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=4w24 4w24], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w25 4w25], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwy 1vwy], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vwz 1vwz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j72 3j72]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J7Q 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='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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j7o|3j7o]], [[3j7p|3j7p]], [[3j7r|3j7r]]</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=3j7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7q OCA], [http://pdbe.org/3j7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j7q RCSB], [http://www.ebi.ac.uk/pdbsum/3j7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7q ProSAT]</span></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=3j7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7q OCA], [http://pdbe.org/3j7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j7q RCSB], [http://www.ebi.ac.uk/pdbsum/3j7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7q ProSAT]</span></td></tr>
 </table>
 == Function ==

3j7q

From Proteopedia

Revision as of 18:06, 10 April 2020

Structure of the idle mammalian ribosome-Sec61 complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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