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| | <SX load='5wlc' size='340' side='right' viewer='molstar' caption='[[5wlc]], [[Resolution|resolution]] 3.80Å' scene=''> | | <SX load='5wlc' size='340' side='right' viewer='molstar' caption='[[5wlc]], [[Resolution|resolution]] 3.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wlc]] is a 70 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_by4741 Saccharomyces cerevisiae by4741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WLC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wlc]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_BY4741 Saccharomyces cerevisiae BY4741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WLC FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.8Å</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='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=5wlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlc OCA], [https://pdbe.org/5wlc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wlc RCSB], [https://www.ebi.ac.uk/pdbsum/5wlc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlc 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=5wlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlc OCA], [http://pdbe.org/5wlc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wlc RCSB], [http://www.ebi.ac.uk/pdbsum/5wlc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/NAT10_YEAST NAT10_YEAST]] RNA cytidine acetyltransferase with specificity toward both 18S rRNA and tRNAs. Catalyzes the formation of N(4)-acetylcytidine (ac4C) at positions 1280 and 1773 in 18S rRNA. Required for early nucleolar cleavages of precursor rRNA at sites A0, A1 and A2 during 18S rRNA synthesis (PubMed:25086048, PubMed:25653167). Catalyzes the formation of ac4C at position 12 in serine and leucine tRNAs. Requires the tRNA-binding adapter protein TAN1 for full tRNA acetyltransferase activity but not for 18S rRNA acetylation (PubMed:25653167).[HAMAP-Rule:MF_03211]<ref>PMID:25086048</ref> <ref>PMID:25653167</ref> [[http://www.uniprot.org/uniprot/RRT14_YEAS6 RRT14_YEAS6]] Involved in ribosome biogenesis, probably through modulation of rDNA transcription. [[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/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/UTP15_YEAST UTP15_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).<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> [[http://www.uniprot.org/uniprot/UTP17_YEAST UTP17_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).<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAS1 KRR1_YEAS1]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth (By similarity).[UniProtKB:P25586] [[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/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/NOP14_YEAST NOP14_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Has a role in the nuclear export of 40S pre-ribosomal subunit to the cytoplasm.<ref>PMID:12068309</ref> <ref>PMID:12446671</ref> [[http://www.uniprot.org/uniprot/UTP5_YEAST UTP5_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).<ref>PMID:12068309</ref> <ref>PMID:15489292</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/UTP7_YEAST UTP7_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/SAS10_YEAST SAS10_YEAST]] Primarily required at the G2/M phase. Essential for viability: involved in nucleolar processing of pre-18S ribosomal RNA as part of the ribosomal small subunit (SSU) processome.<ref>PMID:12068309</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/UTP11_YEAS6 UTP11_YEAS6]] Involved in nucleolar processing of pre-18S ribosomal RNA. [[http://www.uniprot.org/uniprot/DCA13_YEAST DCA13_YEAST]] Required for ribosomal RNA processing.<ref>PMID:8508778</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/FCF2_YEAST FCF2_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/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/UTP14_YEAST UTP14_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/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/NOP56_YEAST NOP56_YEAST]] Required for 60S ribosomal subunit synthesis.<ref>PMID:9372940</ref> [[http://www.uniprot.org/uniprot/UTP9_YEAST UTP9_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).<ref>PMID:12068309</ref> <ref>PMID:15489292</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/NOL10_YEAST NOL10_YEAST]] May be involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</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/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/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/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> [[http://www.uniprot.org/uniprot/UTP6_YEAST UTP6_YEAST]] Component of the SSU processome, a pre-ribosomal particle required for the maturation of the 18S rRNA from the 35S pre-rRNA precursor.<ref>PMID:12068309</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/UTP4_YEAST UTP4_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).<ref>PMID:12068309</ref> <ref>PMID:15489292</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/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/LCP5_YEAST LCP5_YEAST]] Component of the U3 small nucleolar ribonucleoprotein. Required for the early cleavages at sites A0, A1 and A2 of the pre-ribosomal RNA. Participates in ribosome biogenesis. [[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/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/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/FAF1_YEAST FAF1_YEAST]] Required for pre-rRNA processing and 40S ribosomal subunit assembly. Seems to act in the processing of 35S rRNA at the A(0), A(1), and A(2) cleavage sites. [[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/MPP10_YEAST MPP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:15489263</ref> <ref>PMID:9315638</ref> [[http://www.uniprot.org/uniprot/BUD21_YEAST BUD21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Has a role in bud site selection maybe via the regulation of expression of bipolar budding components.<ref>PMID:11452010</ref> <ref>PMID:12068309</ref> [[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>
| + | [https://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] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 A, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.
| + | |
| - | | + | |
| - | The complete structure of the small-subunit processome.,Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S Nat Struct Mol Biol. 2017 Sep 25. doi: 10.1038/nsmb.3472. PMID:28945246<ref>PMID:28945246</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5wlc" style="background-color:#fffaf0;"></div>
| + | |
| - | | + | |
| - | ==See Also==
| + | |
| - | *[[Ribosome 3D structures|Ribosome 3D structures]]
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Saccharomyces cerevisiae by4741]] | + | [[Category: Saccharomyces cerevisiae BY4741]] |
| - | [[Category: RRNA small subunit pseudouridine methyltransferase Nep1]]
| + | [[Category: Barandun J]] |
| - | [[Category: Barandun, J]] | + | [[Category: Chaker-Margot M]] |
| - | [[Category: Chaker-Margot, M]] | + | [[Category: Hunziker M]] |
| - | [[Category: Hunziker, M]] | + | [[Category: Klinge S]] |
| - | [[Category: Klinge, S]] | + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Ribosome assembly]]
| + | |
