5wyk | pdb_00005wyk

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Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)

spinqualitylabelsall models 5wyk, resolution 4.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5wyk is a 58 chain structure with sequence from Saccharomyces cerevisiae (strain atcc 204508 / s288c). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. NonStd Res: UNK Related: 5wyj Activity: rRNA small subunit pseudouridine methyltransferase Nep1, with EC number 2.1.1.260 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Warning: this is a large structure, and loading might take a long time or not happen at all. Function [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. [IMP3_YEAST] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing. [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). [UTP12_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA. [UTP13_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA. [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. [PWP2_YEAST] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA. [IMP4_YEAST] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing. [KRR1_YEAST] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth. [UTP21_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [UTP22_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [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. [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. [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. [NOP56_YEAST] Required for 60S ribosomal subunit synthesis. [RS7A_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [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. [RS14A_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [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. [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. [RL1D1_YEAST] Involved in rRNA-processing and ribosome biosynthesis. [RS9A_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [NOP58_YEAST] Required for pre-18S rRNA processing. May bind microtubules. [UTP18_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. [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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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