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| {{Large structure}}
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| ==Complex of yeast 80S ribosome with non-modified eIF5A== | | ==Complex of yeast 80S ribosome with non-modified eIF5A== |
| <StructureSection load='5dc3' size='340' side='right' caption='[[5dc3]], [[Resolution|resolution]] 3.25Å' scene=''> | | <StructureSection load='5dc3' size='340' side='right'caption='[[5dc3]], [[Resolution|resolution]] 3.25Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[5dc3]] is a 163 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae], [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DC3 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[5dc3]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DC3 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">X-ray diffraction, [[Resolution|Resolution]] 3.25Å</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=5dc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dc3 OCA], [http://pdbe.org/5dc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dc3 RCSB], [http://www.ebi.ac.uk/pdbsum/5dc3 PDBsum]</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=5dc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dc3 OCA], [https://pdbe.org/5dc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dc3 RCSB], [https://www.ebi.ac.uk/pdbsum/5dc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dc3 ProSAT]</span></td></tr> |
| </table> | | </table> |
| {{Large structure}}
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| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RS27A_YEAST RS27A_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). 40S ribosomal protein S31 is a component of the 40S subunit of the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS19A_YEAST RS19A_YEAST]] Required for proper maturation of the small (40S) ribosomal subunit. Binds to 40s pre-ribosomal particles, probably required after association of NOC4 but before association of ENP1, TSR1 and RIO2 with 20/21S pre-rRNA.<ref>PMID:16159874</ref> <ref>PMID:17726054</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[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/RS18A_YEAST RS18A_YEAST]] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity).[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/STM1_YEAST STM1_YEAST]] Binds specifically G4 quadruplex (these are four-stranded right-handed helices, stabilized by guanine base quartets) and purine motif triplex (characterized by a third, antiparallel purine-rich DNA strand located within the major groove of a homopurine stretch of duplex DNA) nucleic acid structures. These structures may be present at telomeres or in rRNAs. Acts with CDC13 to control telomere length homeostasis. Involved in the control of the apoptosis-like cell death.<ref>PMID:15044472</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RL11B_YEAST RL11B_YEAST]] Binds to 5S ribosomal RNA. [[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/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/RS15_YEAST RS15_YEAST]] Involved in the nuclear export of the small ribosomal subunit. Has a role in the late stage of the assembly of pre-40S particles within the nucleus and controls their export to the cytoplasm.<ref>PMID:15167894</ref> [[http://www.uniprot.org/uniprot/RSSA1_YEAST RSSA1_YEAST]] 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.<ref>PMID:9973221</ref> <ref>PMID:14627813</ref> [[http://www.uniprot.org/uniprot/RLA0_YEAST RLA0_YEAST]] Ribosomal protein P0 is the functional equivalent of E.coli protein L10. [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/RS21A_YEAST RS21A_YEAST]] Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Has a physiological role leading to 18S rRNA stability.<ref>PMID:14627813</ref> [[http://www.uniprot.org/uniprot/IF5A1_YEAST IF5A1_YEAST]] mRNA-binding protein involved in translation elongation. Has an important function at the level of mRNA turnover, probably acting downstream of decapping. Involved in actin dynamics and cell cycle progression, mRNA decay and probably in a pathway involved in stress response and maintenance of cell wall integrity. Essential for polarized growth, a process necessary for G1/S transition. May mediate large range of effects of the polyamine spermidine in the cell.<ref>PMID:10229683</ref> <ref>PMID:16157662</ref> <ref>PMID:16408210</ref> <ref>PMID:16914118</ref> <ref>PMID:19338753</ref> <ref>PMID:19424157</ref> <ref>PMID:641056</ref> <ref>PMID:8307948</ref> <ref>PMID:9582285</ref> [[http://www.uniprot.org/uniprot/RS7A_YEAST RS7A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RS6A_YEAST RS6A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RS2_YEAST RS2_YEAST]] Important in the assembly and function of the 40S ribosomal subunit. Mutations in this protein affects the control of translational fidelity. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/GBLP_YEAST GBLP_YEAST]] Located at the head of the 40S ribosomal subunit in the vicinity of the mRNA exit channel, it serves as a scaffold protein that can recruit other proteins to the ribosome. Involved in the negative regulation of translation of a specific subset of proteins.<ref>PMID:15340087</ref> | | [https://www.uniprot.org/uniprot/RSSA1_YEAST RSSA1_YEAST] 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.<ref>PMID:9973221</ref> <ref>PMID:14627813</ref> |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| </div> | | </div> |
| <div class="pdbe-citations 5dc3" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5dc3" style="background-color:#fffaf0;"></div> |
| | |
| | ==See Also== |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | *[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Saccharomyces cerevisiae]] | | [[Category: Large Structures]] |
| [[Category: Saccharomyces cerevisiae s288c]] | | [[Category: Saccharomyces cerevisiae S288C]] |
| [[Category: Dever, T E]] | | [[Category: Dever TE]] |
| [[Category: Mailliot, J]] | | [[Category: Mailliot J]] |
| [[Category: Melnikov, S]] | | [[Category: Melnikov S]] |
| [[Category: Micura, R]] | | [[Category: Micura R]] |
| [[Category: Rigger, L]] | | [[Category: Rigger L]] |
| [[Category: Shin, B S]] | | [[Category: Shin B-S]] |
| [[Category: Yusupov, M]] | | [[Category: Yusupov M]] |
| [[Category: Yusupova, G]] | | [[Category: Yusupova G]] |
| [[Category: Complex]]
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| [[Category: Eif5a]]
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| [[Category: Ribosome]]
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