- EMDB-11358: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
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Basic information
Entry
Database: EMDB / ID: EMD-11358
Title
Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2
Map data
Sample
90S pre-ribosome state B2
Periodic tryptophan protein 2
(Nucleolar complex protein ...) x 2
Something about silencing protein 10
(U3 small nucleolar RNA-associated protein ...) x 17
Bud site selection protein 21
NET1-associated nuclear protein 1
(rRNA-processing protein ...) x 2
(Ribosome biogenesis protein ...) x 3
rRNA 2'-O-methyltransferase fibrillarin
(Nucleolar protein ...Nucleolus) x 2
13 kDa ribonucleoprotein-associated protein
(Ribosomal RNA-processing protein ...) x 2
(U3 small nucleolar ribonucleoprotein protein ...) x 3
RNA 3'-terminal phosphate cyclase-like protein
RNA cytidine acetyltransferase
Ribosomal RNA small subunit methyltransferase NEP1
Essential nuclear protein 1
Pre-rRNA-processing protein PNO1
Protein BFR2
Protein FAF1
KRR1 small subunit processome component
Protein SOF1
Regulator of rDNA transcription protein 14
(40S ribosomal protein ...) x 16
Rps5p
(nucleic-acidNucleic acid) x 3
(ligand) x 2
Function / homology
Function and homology information
rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / tRNA acetylation / UTP-C complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process ...rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / tRNA acetylation / UTP-C complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / mRNA modification / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / septum digestion after cytokinesis / rRNA 2'-O-methylation / rRNA modification / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / box C/D RNP complex / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / small nuclear ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / vesicle-mediated transport / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / protein transport / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
NOP5, N-terminal / BP28, C-terminal domain / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / NUC153 / Ribosomal protein S13/S15, N-terminal / Apoptosis-antagonizing transcription factor, C-terminal ...NOP5, N-terminal / BP28, C-terminal domain / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / NUC153 / Ribosomal protein S13/S15, N-terminal / Apoptosis-antagonizing transcription factor, C-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal domain / NOSIC / Ribosomal protein S13-like, H2TH / U3 snoRNA associated / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Small-subunit processome, Utp13 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / Quinoprotein alcohol dehydrogenase-like superfamily / S15/NS1, RNA-binding / Armadillo-type fold / Ribosomal protein S5/S7, eukaryotic/archaeal / PIN domain / RNA-binding S4 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / NOL6/Upt22 / CCAAT-binding factor / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / KOW / Bystin / Ribosomal protein S12/S23 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Nucleolar protein 14 / Sof1-like protein / Small-subunit processome, Utp21 / Helicase domain / WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase type 2 / Nrap protein, domain 5 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Anaphase-promoting complex subunit 4, WD40 domain / AATF leucine zipper-containing domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / Alpha/beta knot methyltransferases / Ribosomal RNA assembly KRR1 / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Regulator of rDNA transcription 14 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal protein S7 domain / WD40-repeat-containing domain / WD40 repeat, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site
U3 small nucleolar RNA-associated protein 21 / NET1-associated nuclear protein 1 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 5 / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 8 ...U3 small nucleolar RNA-associated protein 21 / NET1-associated nuclear protein 1 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 5 / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 22 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 13 / Nucleolar protein 56 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / Protein BFR2 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Protein FAF1 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Nucleolar complex protein 14 / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S1-A / Regulator of rDNA transcription protein 14 / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S18-A / rRNA 2'-O-methyltransferase fibrillarin / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 18 / Periodic tryptophan protein 2 / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / 40S ribosomal protein S27-A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar ribonucleoprotein protein LCP5 / Pre-rRNA-processing protein PNO1
Journal: Science / Year: 2020 Title: 90 pre-ribosome transformation into the primordial 40 subunit. Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
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