<table><tr><td colspan='2'>[[3j7p]] is a 82 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=4w21 4w21], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w22 4w22], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w23 4w23], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx3 1vx3], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx4 1vx4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx5 1vx5] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j74 3j74]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J7P FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3j7p]] is a 82 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=4w21 4w21], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w22 4w22], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4w23 4w23], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx3 1vx3], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx4 1vx4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vx5 1vx5] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j74 3j74]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J7P FirstGlance]. <br>
[[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> [[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/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/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/B6V8C8_PIG B6V8C8_PIG]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122]
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[[https://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/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). [[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). [[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/B6V8C8_PIG B6V8C8_PIG]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122]
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== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Revision as of 03:51, 21 April 2022
Structure of the 80S mammalian ribosome bound to eEF2
3j7p is a 82 chain structure with sequence from Sus scrofa. This structure supersedes the now removed PDB entries 4w21, 4w22, 4w23, 1vx3, 1vx4, 1vx5 and 3j74. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
[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).[1] [RS18_PIG] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (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). [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). [B6V8C8_PIG] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
↑ Tio PH, Jong WW, Cardosa MJ. Two dimensional VOPBA reveals laminin receptor (LAMR1) interaction with dengue virus serotypes 1, 2 and 3. Virol J. 2005 Mar 25;2:25. PMID:15790424 doi:http://dx.doi.org/10.1186/1743-422X-2-25
↑ 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
