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 / 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 ...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 / 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 / mRNA modification / 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 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 / 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 / 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 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / vesicle-mediated transport / 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 / protein transport / ribosome biogenesis / 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
Ribosomal protein S13/S15, N-terminal / Apoptosis-antagonizing transcription factor, C-terminal / Small-subunit processome, Utp21 / Helicase domain / Bystin / S15/NS1, RNA-binding / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Tetratricopeptide-like helical domain superfamily ...Ribosomal protein S13/S15, N-terminal / Apoptosis-antagonizing transcription factor, C-terminal / Small-subunit processome, Utp21 / Helicase domain / Bystin / S15/NS1, RNA-binding / Quinoprotein alcohol dehydrogenase-like superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Nucleolar protein 14 / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / 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 / Sof1-like protein / Small-subunit processome, Utp12 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S24e / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / 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 biogenesis, methyltransferase, EMG1/NEP1 / Sas10/Utp3/C1D / NOL6/Upt22 / 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 / Small-subunit processome, Utp13 / Ribosomal protein S6, eukaryotic / Nrap protein, domain 3 / Ribosomal protein S17, archaeal/eukaryotic / 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 / AATF leucine zipper-containing domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S28e conserved site / Ribosomal protein S4/S9 / 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 / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / RNA-binding domain, S1 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S8e, 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 / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site
Ribosomal RNA small subunit methyltransferase NEP1 / RNA cytidine acetyltransferase / 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 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 ...Ribosomal RNA small subunit methyltransferase NEP1 / RNA cytidine acetyltransferase / 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 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Nucleolar protein 58 / 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 / Nucleolar protein 56 / U3 small nucleolar RNA-associated protein 22 / 40S ribosomal protein S28-A / 40S ribosomal protein S22-B / U3 small nucleolar RNA-associated protein 8 / Protein SOF1 / Ribosome biogenesis protein ENP2 / Periodic tryptophan protein 2 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-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 / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S5 / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / 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 / U3 small nucleolar ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / Nucleolar complex protein 14
National Natural Science Foundation of China (NSFC)
91940302, 91540201, 31430024, 31325007
China
Chinese Academy of Sciences
XDB08010203
China
Citation
Journal: Science / Year: 2020 Title: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states. Authors: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye / Abstract: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by ...The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression.
3A: U3 snoRNA 5A: 5' ETS SA: 18S pre-rRNA SC: 40S ribosomal protein S1-A SF: 40S ribosomal protein S4-A SG: 40S ribosomal protein S5 SH: 40S ribosomal protein S6-A SI: 40S ribosomal protein S7-A SJ: 40S ribosomal protein S8-A SK: 40S ribosomal protein S9-A SM: 40S ribosomal protein S11-A SO: 40S ribosomal protein S13 SP: 40S ribosomal protein S14-A SR: 40S ribosomal protein S16-A SX: 40S ribosomal protein S22-B SY: 40S ribosomal protein S23-A SZ: 40S ribosomal protein S24-A Sc: 40S ribosomal protein S27-A Sd: 40S ribosomal protein S28-A 3B: rRNA 2'-O-methyltransferase fibrillarin 3C: rRNA 2'-O-methyltransferase fibrillarin 3D: Nucleolar protein 56 3E: Nucleolar protein 58 3F: Ribosomal RNA-processing protein 9 3G: 13 kDa ribonucleoprotein-associated protein 3H: 13 kDa ribonucleoprotein-associated protein A4: U3 small nucleolar RNA-associated protein 4 A5: U3 small nucleolar RNA-associated protein 5 A8: U3 small nucleolar RNA-associated protein 8 A9: U3 small nucleolar RNA-associated protein 9 AE: U3 small nucleolar RNA-associated protein 10 AF: U3 small nucleolar RNA-associated protein 15 AG: NET1-associated nuclear protein 1 B1: Periodic tryptophan protein 2 B2: U3 small nucleolar RNA-associated protein 12 B3: U3 small nucleolar RNA-associated protein 13 B8: U3 small nucleolar RNA-associated protein 18 BE: U3 small nucleolar RNA-associated protein 21 B6: U3 small nucleolar RNA-associated protein 6 5B: Bud site selection protein 21 5C: U3 small nucleolar RNA-associated protein 7 5D: U3 small nucleolar RNA-associated protein 11 5E: U3 small nucleolar RNA-associated protein MPP10 5F: U3 small nucleolar ribonucleoprotein protein IMP3 5G: U3 small nucleolar ribonucleoprotein protein IMP4 5H: Something about silencing protein 10 5I: Protein SOF1 5J: rRNA-processing protein FCF2 5K: rRNA-processing protein FCF1 RA: Ribosome biogenesis protein ENP2 RB: U3 small nucleolar ribonucleoprotein protein LCP5 RD: rRNA biogenesis protein RRP5 RE: U3 small nucleolar RNA-associated protein 22 RF: Ribosomal RNA-processing protein 7 RG: Ribosomal RNA small subunit methyltransferase NEP1 RH: Ribosomal RNA small subunit methyltransferase NEP1 RJ: Ribosome biogenesis protein BMS1 RK: RNA 3'-terminal phosphate cyclase-like protein RL: RNA cytidine acetyltransferase RM: RNA cytidine acetyltransferase RN: Nucleolar complex protein 14 RO: Nucleolar complex protein 4 RP: U3 small nucleolar RNA-associated protein 20 RQ: U3 small nucleolar RNA-associated protein 14 RS: Essential nuclear protein 1 RT: Pno1 RY: Protein BFR2 X1: Unassigned helices hetero molecules
Mass: 7605.847 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: Q3E7X9
+
Protein , 15 types, 19 molecules 3B3C3G3HAGB15B5H5IRDRGRHRKRLRMRSRTRYX1
#20: Protein
rRNA2'-O-methyltransferasefibrillarin / Nop1 / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 ...Nop1 / 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
#24: Protein
13kDaribonucleoprotein-associatedprotein / Snu13 / 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
#31: 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
#32: 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
#38: 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
#44: 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
#45: Protein
ProteinSOF1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1
Mass: 56888.918 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: P33750
#50: 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
Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 18028
Image scans
Movie frames/image: 32 / Used frames/image: 1-32
-
Processing
EM software
ID
Name
Version
Category
3
CTFFIND
4.1.8
CTFcorrection
7
RELION
initialEulerassignment
8
RELION
finalEulerassignment
9
RELION
classification
10
RELION
3Dreconstruction
17
UCSF Chimera
modelfitting
18
Coot
modelfitting
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 382298
3D reconstruction
Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3050 / Symmetry type: POINT
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