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| | <SX load='5wyj' size='340' side='right' viewer='molstar' caption='[[5wyj]], [[Resolution|resolution]] 8.70Å' scene=''> | | <SX load='5wyj' size='340' side='right' viewer='molstar' caption='[[5wyj]], [[Resolution|resolution]] 8.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wyj]] is a 64 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WYJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WYJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wyj]] is a 12 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=5WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WYJ FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 8.7Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </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=5wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyj OCA], [https://pdbe.org/5wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wyj RCSB], [https://www.ebi.ac.uk/pdbsum/5wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyj 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=5wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyj OCA], [http://pdbe.org/5wyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyj RCSB], [http://www.ebi.ac.uk/pdbsum/5wyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RRP5_YEAST RRP5_YEAST]] Involved in the biogenesis of rRNA. Required for the formation of 18S and 5.8S rRNA.<ref>PMID:8896463</ref> [[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/ENP1_YEAST ENP1_YEAST]] Required for normal export of the pre-40S particles from the nucleus to the cytoplasm. Its subcellular location and association with pre-40S subunit shifts from mixed cytoplasm/nucleus to all nuclear in RPS19 disruptions, suggesting it acts after the ribosomal protein.<ref>PMID:12628929</ref> <ref>PMID:16159874</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[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/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</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/NOP56_YEAST NOP56_YEAST]] Required for 60S ribosomal subunit synthesis.<ref>PMID:9372940</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</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/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</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/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</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/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref> | + | [https://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 22: |
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| | ==See Also== | | ==See Also== |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] | | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| - | *[[Ribosome biogenesis protein|Ribosome biogenesis protein]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Baker's yeast]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RRNA small subunit pseudouridine methyltransferase Nep1]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Sun, Q]] | + | [[Category: Sun Q]] |
| - | [[Category: Ye, K]] | + | [[Category: Ye K]] |
| - | [[Category: Zhu, X]] | + | [[Category: Zhu X]] |
| - | [[Category: Pre-ribosome]]
| + | |
| - | [[Category: Protein-rna complex]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| Structural highlights
Function
FBRL_YEAST S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).[1] [2] [3]
Publication Abstract from PubMed
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
Molecular architecture of the 90S small subunit pre-ribosome.,Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K Elife. 2017 Feb 28;6. pii: e22086. doi: 10.7554/eLife.22086. PMID:28244370[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tollervey D, Lehtonen H, Carmo-Fonseca M, Hurt EC. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 1991 Mar;10(3):573-83. PMID:1825809
- ↑ Tessarz P, Santos-Rosa H, Robson SC, Sylvestersen KB, Nelson CJ, Nielsen ML, Kouzarides T. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature. 2014 Jan 23;505(7484):564-8. doi: 10.1038/nature12819. Epub 2013 Dec 18. PMID:24352239 doi:http://dx.doi.org/10.1038/nature12819
- ↑ Schimmang T, Tollervey D, Kern H, Frank R, Hurt EC. A yeast nucleolar protein related to mammalian fibrillarin is associated with small nucleolar RNA and is essential for viability. EMBO J. 1989 Dec 20;8(13):4015-24. PMID:2686980
- ↑ Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. Elife. 2017 Feb 28;6. pii: e22086. doi: 10.7554/eLife.22086. PMID:28244370 doi:http://dx.doi.org/10.7554/eLife.22086
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