18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / 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 / 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 / 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) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / proteasome assembly / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / positive regulation of translational fidelity / maintenance 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 / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / mitochondrial matrix / RNA helicase activity / translation / cell cycle / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding
Fcf1 / 30s ribosomal protein S13, C-terminal / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / P-loop containing nucleoside triphosphate hydrolase ...Fcf1 / 30s ribosomal protein S13, C-terminal / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / P-loop containing nucleoside triphosphate hydrolase / 50S ribosomal protein L30e-like / Nucleolar complex protein 4 / Periodic tryptophan protein 2 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal protein S7 domain / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S15P / RNA-binding domain, S1 / S-adenosyl-L-methionine-dependent methyltransferase / Bms1/Tsr1-type G domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Winged helix DNA-binding domain superfamily / Nop domain superfamily / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S8 superfamily / Nrap protein, domain 6 / Nrap protein, domain 5 / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Nrap protein domain 1 / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4/S9 / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S19e domain superfamily / Ribosomal protein S6, eukaryotic / WD40-repeat-containing domain / RNA 3'-terminal phosphate cyclase type 2 / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / Fcf2 pre-rRNA processing, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Helicase superfamily 1/2, ATP-binding domain / Ribosomal S24e conserved site / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp13 / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / RNA 3'-terminal phosphate cyclase, insert domain / U3 snoRNA associated / NOSIC / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / HEAT, type 2 / Ribosomal protein S17, conserved site / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S7, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Ribosomal protein S4e, N-terminal, conserved site / U3 small nucleolar RNA-associated protein 15, C-terminal / U3 small nucleolar RNA-associated protein 8 / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S13, conserved site / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / BP28, C-terminal domain / EMG1/NEP1 methyltransferase / Dip2/Utp12 Family / Sof1-like domain / Fcf2 pre-rRNA processing / Ribosomal RNA adenine dimethylase / Krr1 KH1 domain / S1 RNA binding domain / Bystin / Oligonucleotide/oligosaccharide-binding (OB)-fold / Sas10/Utp3/C1D family / Helicase associated domain (HA2) / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Ribosomal protein S28e
rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / Ribosomal RNA-processing protein 9 / 40S ribosomal protein S18-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A ...rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / Ribosomal RNA-processing protein 9 / 40S ribosomal protein S18-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S22-A / 40S ribosomal protein S19-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / 40S ribosomal protein S5 / Periodic tryptophan protein 2 / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S1-A / Nucleolar protein 58 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Pre-rRNA-processing protein PNO1 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / Nucleolar protein 56 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 12 / Something about silencing protein 10 / rRNA-processing protein FCF2 / Ribosome biogenesis protein BMS1 / Bud site selection protein 21 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 4 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 15 / Protein SOF1 / U3 small nucleolar RNA-associated protein 18 / Nucleolar complex protein 4 / 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 / Dimethyladenosine transferase / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / 40S ribosomal protein S7-A
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.
UA: Periodic tryptophan protein 2 UB: Nucleolar complex protein 14 UC: Something about silencing protein 10 UD: U3 small nucleolar RNA-associated protein 4 UE: U3 small nucleolar RNA-associated protein 5 UF: U3 small nucleolar RNA-associated protein 6 UG: U3 small nucleolar RNA-associated protein 7 UH: U3 small nucleolar RNA-associated protein 8 UI: U3 small nucleolar RNA-associated protein 9 UJ: U3 small nucleolar RNA-associated protein 10 UK: U3 small nucleolar RNA-associated protein 11 UL: U3 small nucleolar RNA-associated protein 12 UM: U3 small nucleolar RNA-associated protein 13 UN: U3 small nucleolar RNA-associated protein 14 UO: U3 small nucleolar RNA-associated protein 15 UP: Bud site selection protein 21 UQ: NET1-associated nuclear protein 1 UR: U3 small nucleolar RNA-associated protein 18 US: Nucleolar complex protein 4 UT: U3 small nucleolar RNA-associated protein 20 UU: U3 small nucleolar RNA-associated protein 21 UV: U3 small nucleolar RNA-associated protein 22 UX: rRNA-processing protein FCF1 CA: rRNA 2'-O-methyltransferase fibrillarin CB: rRNA 2'-O-methyltransferase fibrillarin CD: Nucleolar protein 56 CE: Nucleolar protein 58 CF: 13 kDa ribonucleoprotein-associated protein CG: 13 kDa ribonucleoprotein-associated protein CH: Ribosomal RNA-processing protein 9 CI: U3 small nucleolar ribonucleoprotein protein IMP3 CJ: U3 small nucleolar ribonucleoprotein protein IMP4 CK: U3 small nucleolar RNA-associated protein MPP10 CL: Ribosome biogenesis protein BMS1 CM: RNA 3'-terminal phosphate cyclase-like protein CN: Ribosomal RNA-processing protein 7 JD: Probable ATP-dependent RNA helicase DHR1 JF: Ribosomal RNA small subunit methyltransferase NEP1 JG: Ribosomal RNA small subunit methyltransferase NEP1 JH: Essential nuclear protein 1 JI: rRNA biogenesis protein RRP5 JL: Dimethyladenosine transferase JM: rRNA-processing protein FCF2 JP: Protein SOF1 Db: 40S ribosomal protein S27-A JJ: Pre-rRNA-processing protein PNO1 DA: 40S ribosomal protein S1-A DE: 40S ribosomal protein S4-A DF: Rps5p DG: 40S ribosomal protein S6-A DH: 40S ribosomal protein S7-A DI: 40S ribosomal protein S8-A DJ: 40S ribosomal protein S9-A DL: 40S ribosomal protein S11-A DN: 40S ribosomal protein S13 DO: 40S ribosomal protein S14-A DQ: 40S ribosomal protein S16-A DS: 40S ribosomal protein S18-A DT: 40S ribosomal protein S19-A DW: 40S ribosomal protein S22-A DX: 40S ribosomal protein S23-A DY: 40S ribosomal protein S24-A Dc: 40S ribosomal protein S28-A D2: 5ETS RNA D3: 18S rRNA D4: U3 snoRNA hetero molecules
Protein , 16 types, 19 molecules UAUCUPUQCACBCFCGCLCMJDJFJGJHJIJLJPJJDF
#1: Protein
Periodictryptophanprotein2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1
Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P25635
#3: Protein
Somethingaboutsilencingprotein10 / U three protein 3 / U3 small nucleolar RNA-associated protein 3 / U3 snoRNA-associated protein 11
Mass: 70364.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12136
#16: Protein
Budsiteselectionprotein21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16
Mass: 24431.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08492
#17: Protein
NET1-associatednuclearprotein1 / U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA- ...U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA-associated protein 17 / U3 snoRNA-associated protein 17
Mass: 101341.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02931
#24: Protein
rRNA2'-O-methyltransferasefibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1
Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#27: Protein
13kDaribonucleoprotein-associatedprotein / Small nuclear ribonucleoprotein-associated protein 1
Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P39990
#32: Protein
RibosomebiogenesisproteinBMS1 /
Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08965
#33: Protein
RNA3'-terminalphosphatecyclase-likeprotein
Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08096
Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#37: Protein
Essentialnuclearprotein1
Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38333
#38: Protein
rRNAbiogenesisproteinRRP5 / Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA- ...Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA-associated protein RRP5
Mass: 193411.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q05022
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