3jct | pdb_00003jct

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Cryo-em structure of eukaryotic pre-60S ribosomal subunits

spinqualitylabelsall models 3jct, resolution 3.08Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3jct is a 58 chain structure with sequence from Saccharomyces cerevisiae s288c. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GTP, MG, ZN 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 [NSA2_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles. Under normal, rapid growth conditions, high levels of NSA2 would allow the progression of pre-60S particles through the ITS2 processing. [NOG1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. [CGR1_YEAST] Involved in nucleolar integrity and required for processing of the pre-rRNA for the 60S ribosome subunit. [PESC_YEAST] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03028] [RRS1_YEAST] Required for ribosome biogenesis. [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [RL11A_YEAST] Binds to 5S ribosomal RNA. [CIC1_YEAST] An adapter protein that specifically links the 26S proteasome to its substrate CDC4 which is one of the substrate recognition subunits of the SCF E3 ubiquitin ligase complex. Required for turnover of cell cycle regulatory proteins CDC4 and GRR1. Required for synthesis and nuclear export of 60S ribosomal subunits. Required for vegetative growth. [RPF2_YEAST] Required for biogenesis of the 60S ribosomal subunit. [RLP7_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. May act as a specificity factor that binds precursor rRNAs and tethers the enzymes that carry out the early 5' to 3' exonucleolytic reactions that generate the mature rRNAs. [MRT4_YEAST] Involved in mRNA turnover and ribosome assembly. [NLE1_YEAST] Involved in processing and efficient intra-nuclear transport or pre-60S ribosomal subunits. Forms a complex with REA1 which is essential for ATP-dependent dissociation of a group of nonribosomal factors from the pre-60S particle. [NOG2_YEAST] GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation. [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA. [IF6_YEAST] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by the GTPase RIA1/EFL1 and by SDO1. Also required for pre-rRNA processing. [BUD20_YEAST] Involved in positioning the proximal bud pole signal. [NOP15_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Required for pre-rRNA processing and cytokinesis. Associates with the precursors of the 25S and 5.8S rRNAs. [RLP24_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles. [RL5_YEAST] Binds 5S RNA and is required for 60S subunit assembly. [ARX1_YEAST] Probable metalloprotease involved in proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Accompanies the pre-60S particles to the cytoplasm. [NUG1_YEAST] GTPase required for 60S ribosomal subunit export to the cytoplasm. [NOP53_YEAST] Late-acting factor in the nuclear maturation of 60S ribosomal subunits, which is required for normal acquisition of export competence. Required for the export of the large subunit. Acts to stimulate the RNase activity of the exosome complex, and may recruit the exosome to 7S pre-rRNA for processing. Associates with numerous RNAs including the 27S and 7S pre-rRNAs and the box H/ACA snoRNA snR37. Also interacts (via N-terminal region) with the mature 25S rRNA and the mature 5.8S rRNA. Publication Abstract from PubMed Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly. Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes.,Wu S, Tutuncuoglu B, Yan K, Brown H, Zhang Y, Tan D, Gamalinda M, Yuan Y, Li Z, Jakovljevic J, Ma C, Lei J, Dong MQ, Woolford JL Jr, Gao N Nature. 2016 Jun 2;534(7605):133-7. doi: 10.1038/nature17942. PMID:27251291 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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