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- PDB-6lqr: Cryo-EM structure of 90S small subunit preribosomes in transition... -

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Entry
Database: PDB / ID: 6lqr
TitleCryo-EM structure of 90S small subunit preribosomes in transition states (State C)
Components
  • (40S ribosomal protein ...) x 16
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • (rRNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S pre-rRNA
  • 5' ETS
  • Bud site selection protein 21
  • Essential nuclear protein 1
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Pno1
  • Protein BFR2
  • Protein SOF1
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Something about silencing protein 10
  • U3 snoRNA
  • Unassigned helices
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA biogenesis protein RRP5
KeywordsRIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1
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 / 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
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsDu, Y. / Ye, K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91940302, 91540201, 31430024, 31325007 China
Chinese Academy of SciencesXDB08010203 China
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)4,794,07372
Polymers4,793,39568
Non-polymers6784
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 3A5ASA

#1: RNA chain U3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#2: RNA chain 5' ETS


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#3: RNA chain 18S pre-rRNA


Mass: 582710.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

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40S ribosomal protein ... , 16 types, 16 molecules SCSFSGSHSISJSKSMSOSPSRSXSYSZScSd

#4: Protein 40S ribosomal protein S1-A / Ribosome / Rps1 / RP10A


Mass: 28798.467 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: P33442
#5: Protein 40S ribosomal protein S4-A / Ribosome / Rps4 / RP5 / S7 / YS6


Mass: 29469.330 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: P0CX35
#6: Protein 40S ribosomal protein S5 / / Rps5 / RP14 / S2 / YS8


Mass: 25072.600 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: P26783
#7: Protein 40S ribosomal protein S6-A / Ribosome / Rps6 / RP9 / S10 / YS4


Mass: 27054.486 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: P0CX37
#8: Protein 40S ribosomal protein S7-A / Ribosome / Rps7 / RP30 / RP40


Mass: 21658.209 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: P26786
#9: Protein 40S ribosomal protein S8-A / Ribosome / Rps8 / RP19 / S14 / YS9


Mass: 22537.803 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: P0CX39
#10: Protein 40S ribosomal protein S9-A / Ribosome / Rps9 / RP21 / S13 / YP28 / YS11


Mass: 22487.893 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: O13516
#11: Protein 40S ribosomal protein S11-A / Ribosome / Rps11 / RP41 / S18 / YS12


Mass: 17785.934 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: P0CX47
#12: Protein 40S ribosomal protein S13 / / Rps13 / S27a / YS15


Mass: 17059.945 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: P05756
#13: Protein 40S ribosomal protein S14-A / Ribosome / Rps14 / RP59A


Mass: 14562.655 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: P06367
#14: Protein 40S ribosomal protein S16-A / Ribosome / Rps16 / RP61R


Mass: 15877.490 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: P0CX51
#15: Protein 40S ribosomal protein S22-B / Ribosome / Rps22 / RP50 / S24 / Small ribosomal subunit protein uS8-B / YP58 / YS22


Mass: 14650.062 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: Q3E7Y3
#16: Protein 40S ribosomal protein S23-A / Ribosome / Rps23 / RP37 / S28 / YS14


Mass: 16073.896 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: P0CX29
#17: Protein 40S ribosomal protein S24-A / Ribosome / Rps24 / RP50


Mass: 15362.848 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: P0CX31
#18: Protein 40S ribosomal protein S27-A / Ribosome / Rps27 / RP61 / YS20


Mass: 8893.391 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: P35997
#19: Protein 40S ribosomal protein S28-A / Ribosome / Rps28 / S33 / YS27


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

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Protein , 15 types, 19 molecules 3B3C3G3HAGB15B5H5IRDRGRHRKRLRMRSRTRYX1

#20: Protein rRNA 2'-O-methyltransferase fibrillarin / 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 13 kDa ribonucleoprotein-associated protein / 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-associated nuclear protein 1 / 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 Periodic tryptophan protein 2 / 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 Bud site selection protein 21 / 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 Something about silencing protein 10 / 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 Protein SOF1 / 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 rRNA biogenesis protein RRP5 / 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
#53: Protein Ribosomal RNA small subunit methyltransferase NEP1 / / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / ...18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / Essential for mitotic growth protein 1 / Nucleolar essential protein 1


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
#55: Protein RNA 3'-terminal phosphate cyclase-like protein


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
#56: Protein RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine ...18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine acetyltransferase 1


Mass: 119509.445 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: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#61: Protein Essential nuclear protein 1


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
#62: Protein Pno1 /


Mass: 36356.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#63: Protein Protein BFR2 / Brefeldin A resistance protein 2


Mass: 61285.039 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: Q06631
#64: Protein Unassigned helices


Mass: 29549.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

+
Nucleolar protein ... , 2 types, 2 molecules 3D3E

#21: Protein Nucleolar protein 56 / Nucleolus / Nop56 / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1


Mass: 56961.152 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: Q12460
#22: Protein Nucleolar protein 58 / Nucleolus / Nucleolar protein 5


Mass: 57060.344 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: Q12499

+
Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF

#23: Protein Ribosomal RNA-processing protein 9 / Rrp9


Mass: 65146.969 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: Q06506
#52: Protein Ribosomal RNA-processing protein 7


Mass: 34526.441 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: P25368

+
U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERERPRQ

#25: Protein U3 small nucleolar RNA-associated protein 4 / Utp4 / U3 snoRNA-associated protein 4 / U three protein 4 / U3 protein 4 required for transcription / t-UTP4


Mass: 87909.242 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: Q06679
#26: Protein U3 small nucleolar RNA-associated protein 5 / Utp5 / U3 snoRNA-associated protein 5 / U three protein 5 / U3 protein 5 required for transcription / t-UTP5


Mass: 72079.445 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: Q04177
#27: Protein U3 small nucleolar RNA-associated protein 8 / Utp8 / U3 snoRNA-associated protein 8 / U three protein 8 / U3 protein 8 required for transcription / t-UTP8


Mass: 80269.648 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: P53276
#28: Protein U3 small nucleolar RNA-associated protein 9 / Utp9 / U3 snoRNA-associated protein 9 / U three protein 9 / U3 protein 9 required for transcription / t-UTP9


Mass: 65347.254 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: P38882
#29: Protein U3 small nucleolar RNA-associated protein 10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10


Mass: 200298.984 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: P42945
#30: Protein U3 small nucleolar RNA-associated protein 15 / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for transcription / t-UTP15


Mass: 57765.289 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: Q04305
#33: Protein U3 small nucleolar RNA-associated protein 12 / U3 snoRNA-associated protein 12 / DOM34-interacting protein 2 / U three protein 12


Mass: 106481.133 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: Q12220
#34: Protein U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13


Mass: 91132.562 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: Q05946
#35: Protein U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66494.250 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: P40362
#36: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 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: Q06078
#37: Protein U3 small nucleolar RNA-associated protein 6 / U3 snoRNA-associated protein 6 / U three protein 6


Mass: 52495.277 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: Q02354
#39: Protein U3 small nucleolar RNA-associated protein 7 / U3 snoRNA-associated protein 7 / U three protein 7


Mass: 62418.570 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: P40055
#40: Protein U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / U three protein 11


Mass: 29806.348 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: P34247
#41: Protein U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 67042.492 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: P47083
#51: Protein U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 140660.141 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: P53254
#59: Protein U3 small nucleolar RNA-associated protein 20 / U3 snoRNA-associated protein 20 / U three protein 20


Mass: 287915.500 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: P35194
#60: Protein U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14


Mass: 103189.750 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: Q04500

+
U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules 5F5GRB

#42: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 21928.529 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: P32899
#43: Protein U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Interacting with MPP10 protein 4


Mass: 33536.168 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: P53941
#49: Protein U3 small nucleolar ribonucleoprotein protein LCP5


Mass: 40864.391 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: P40079

+
RRNA-processing protein ... , 2 types, 2 molecules 5J5K

#46: Protein rRNA-processing protein FCF2 / FAF1 copurifying factor 2


Mass: 25689.240 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: Q12035
#47: Protein rRNA-processing protein FCF1 / FAF1-copurifying factor 1


Mass: 21650.729 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: Q05498

+
Ribosome biogenesis protein ... , 2 types, 2 molecules RARJ

#48: Protein Ribosome biogenesis protein ENP2 / / Essential nuclear protein 2


Mass: 81864.172 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: P48234
#54: Protein Ribosome biogenesis protein BMS1 /


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

+
Nucleolar complex protein ... , 2 types, 2 molecules RNRO

#57: Protein Nucleolar complex protein 14 / U three protein 2 / U3 small nucleolar RNA-associated protein 2 / U3 snoRNA-associated protein 2


Mass: 94463.195 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: Q99207
#58: Protein Nucleolar complex protein 4 / U three protein 19 / U3 small nucleolar RNA-associated protein 19 / U3 snoRNA-associated protein 19


Mass: 63707.844 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: Q06512

+
Non-polymers , 3 types, 4 molecules

#65: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#66: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#67: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 90S pre-ribosome (Dhr1-depleted, state C) / Type: COMPLEX / Entity ID: #1-#64 / Source: NATURAL
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMpotassium acetateCH3COOK1
220 mMHEPES-KHEPES-K1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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 scansMovie frames/image: 32 / Used frames/image: 1-32

-
Processing

EM software
IDNameVersionCategory
3CTFFIND4.1.8CTF correction
7RELIONinitial Euler assignment
8RELIONfinal Euler assignment
9RELIONclassification
10RELION3D reconstruction
17UCSF Chimeramodel fitting
18Cootmodel fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 382298
3D reconstructionResolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3050 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6LQP

6lqp

+
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