- EMDB-11360: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
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Basic information
Entry
Database: EMDB / ID: EMD-11360
Title
Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1
Map data
Sample
90S pre-ribbosome state Post-A1
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
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 2
Ribosome biogenesis protein BMS1
RNA 3'-terminal phosphate cyclase-like protein
Probable ATP-dependent RNA helicase DHR1
Ribosomal RNA small subunit methyltransferase NEP1
Essential nuclear protein 1
rRNA biogenesis protein RRP5
Dimethyladenosine transferase
Protein SOF1
(40S ribosomal protein ...) x 17
Pre-rRNA-processing protein PNO1
Rps5p
(nucleic-acidNucleic acid) x 3
(ligand) x 3
Function / homology
Function and homology information
18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process ...18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / box C/D RNA binding / box C/D RNA 3'-end processing / Mpp10 complex / box H/ACA snoRNA binding / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / 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 / rDNA heterochromatin / nuclear microtubule / 90S preribosome assembly / 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 / 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 / poly(U) RNA 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) / enzyme activator activity / 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 / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / 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 / ribosome biogenesis / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / tRNA binding / RNA helicase / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / RNA helicase activity / cell cycle / ATPase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding
U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S13/S15, N-terminal / Helicase-associated domain / Bystin / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Ribosomal RNA adenine dimethylase ...U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S13/S15, N-terminal / Helicase-associated domain / Bystin / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Ribosomal RNA adenine dimethylase / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Sof1-like protein / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / U3 snoRNA associated / 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 / Small-subunit processome, Utp21 / Nucleolar protein 14 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein S11 / Ribosomal protein S24e / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Nop domain / PIN domain / RNA-binding S4 domain / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / NOL6/Upt22 / Small-subunit processome, Utp12 / CCAAT-binding factor / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / KOW / 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 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA-binding domain, S1 / Ribosomal protein S15P / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Fibrillarin, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / HEAT, type 2 / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S3Ae, conserved site / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site
Probable ATP-dependent RNA helicase DHR1 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 ...Probable ATP-dependent RNA helicase DHR1 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / 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 / U3 small nucleolar RNA-associated protein 13 / 40S ribosomal protein S28-A / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / 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 / Nucleolar protein 56 / Nucleolar protein 58 / U3 small nucleolar RNA-associated protein 10 / Nucleolar complex protein 14 / U3 small nucleolar RNA-associated protein MPP10 / Periodic tryptophan protein 2 / Dimethyladenosine transferase / 40S ribosomal protein S16-A / 40S ribosomal protein S5 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S19-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 S18-A / U3 small nucleolar RNA-associated protein 18 / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / 40S ribosomal protein S27-A / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / 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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