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- EMDB-0954: Cryo-EM structure of 90S small subunit preribosomes in transition... -

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Basic information

Entry
Database: EMDB / ID: EMD-0954
TitleCryo-EM structure of 90S small subunit preribosomes in transition states (State A1)
Map data
Sample90S pre-ribosome (Dhr1-depleted, state A1)
  • (nucleic-acidNucleic acid) x 3
  • (40S ribosomal protein ...) x 16
  • rRNA 2'-O-methyltransferase fibrillarin
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Bud site selection protein 21
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • Something about silencing protein 10
  • Protein SOF1
  • (rRNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • KRR1 small subunit processome component
  • rRNA biogenesis protein RRP5
  • Ribosomal RNA small subunit methyltransferase NEP1
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • (Nucleolar complex protein ...) x 2
  • Essential nuclear protein 1
  • Pno1
  • Protein FAF1
  • Regulator of rDNA transcription protein 14
  • Protein BFR2
  • Unassigned helices
  • (ligand) x 3
Function / homology
Function and homology information


rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / CURI complex / sno(s)RNA processing / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process ...rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / CURI complex / sno(s)RNA processing / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / histone-glutamine methyltransferase activity / box C/D RNA binding / box C/D RNA 3'-end processing / box H/ACA snoRNA binding / Mpp10 complex / septum digestion after cytokinesis / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / 90S preribosome assembly / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snRNA binding / rRNA primary transcript binding / box C/D RNP complex / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / histone glutamine methylation / U4 snRNA binding / SUMOylation of RNA binding proteins / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / rRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / tRNA export from nucleus / 90S preribosome / O-methyltransferase activity / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / snoRNA binding / rRNA methylation / L13a-mediated translational silencing of Ceruloplasmin expression / 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) / regulation of translational fidelity / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / 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 / enzyme activator activity / translational termination / maintenance of translational fidelity / positive regulation of translational fidelity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / protein transport / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / cell cycle
Similarity search - Function
Regular of rDNA transcription protein 14 / Regulator of rDNA transcription 14 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Apoptosis antagonizing transcription factor / Protein AATF/Bfr2 / NUC153 / NUC153 domain / Nucleolar protein 10/Enp2 ...Regular of rDNA transcription protein 14 / Regulator of rDNA transcription 14 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Apoptosis antagonizing transcription factor / Protein AATF/Bfr2 / NUC153 / NUC153 domain / Nucleolar protein 10/Enp2 / U3 small nucleolar RNA-associated protein 8 / Utp8 family / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Possible tRNA binding domain / Domain of unknown function (DUF1726) / Helicase domain / Helicase / TmcA/NAT10/Kre33 / GNAT acetyltransferase 2 / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / Ribosomal RNA assembly KRR1 / U3 snoRNA associated / Down-regulated in metastasis / Down-regulated-in-metastasis protein / Nucleolar complex protein 4 / U3 snoRNA associated / CBF/Mak21 family / CCAAT-binding factor / Nucleolar protein 14 / Nop14-like family / rRNA-processing protein Fcf1, PIN domain / Nrap protein domain 1 / Nrap protein, domain 3 / Nrap protein domain 1 / Nrap protein, domain 6 / Nrap protein, domain 4 / Nrap protein, domain 5 / Utp11 protein / WD repeat-containing protein WDR46/Utp7 / Small-subunit processome, Utp11 / Nrap protein, domain 2 / Fcf2/DNTTIP2 / Fcf2 pre-rRNA processing, C-terminal / BING4, C-terminal domain / Nrap protein domain 6 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein domain 3 / Nrap protein PAP/OAS-like domain / Sof1-like protein / NOL6/Upt22 / BING4CT (NUC141) domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / Sof1-like domain / U3 small nucleolar RNA-associated protein 6 / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / Ribosomal RNA-processing protein 7, C-terminal domain / U3 small nucleolar RNA-associated protein 6 / Fcf1 / rRNA-processing protein Fcf1/Utp23 / Ribosomal RNA-processing protein 7 / Rrp7 RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Small-subunit processome, Utp14 / Sas10 C-terminal domain / Sas10 C-terminal domain / NOP5, N-terminal / NOP5NT (NUC127) domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / Ribosome biogenesis protein Bms1, N-terminal / Krr1, KH1 domain / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp13 / Krr1 KH1 domain / U3 small nucleolar RNA-associated protein 10, N-terminal / BP28, C-terminal domain / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Ribosomal RNA-processing protein Rrp9-like / Dip2/Utp12 Family / Small-subunit processome, Utp12 / Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain / Bystin / Bystin / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar ribonucleoprotein protein IMP4 ...U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar ribonucleoprotein protein IMP4 / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 4 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / Protein BFR2 / 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 / 40S ribosomal protein S28-A / 40S ribosomal protein S22-B / Ribosome biogenesis protein ENP2 / 40S ribosomal protein S12 / 40S ribosomal protein S24-A / U3 small nucleolar RNA-associated protein MPP10 / 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 S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S18-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / 40S ribosomal protein S5 / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Protein FAF1 / Nucleolar complex protein 14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDu Y / Ye K
Funding support China, 2 items
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.
History
DepositionJan 14, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lqu
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0954.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 448 pix.
= 597.632 Å
1.33 Å/pix.
x 448 pix.
= 597.632 Å
1.33 Å/pix.
x 448 pix.
= 597.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.08180235 - 0.1688727
Average (Standard dev.)0.00045614777 (±0.0041431948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 597.632 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3341.3341.334
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z597.632597.632597.632
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0820.1690.000

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Supplemental data

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Sample components

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Entire 90S pre-ribosome (Dhr1-depleted, state A1)

EntireName: 90S pre-ribosome (Dhr1-depleted, state A1) / Number of Components: 72

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Component #1: protein, 90S pre-ribosome (Dhr1-depleted, state A1)

ProteinName: 90S pre-ribosome (Dhr1-depleted, state A1) / Recombinant expression: No
MassTheoretical: 5 MDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #2: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU ...Sequence:
GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU CUAUAAUUUU GAAUAAAAAU UUUGCUUUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU
MassTheoretical: 106.503258 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: nucleic-acid, 5' ETS

nucleic acidName: 5' ETS / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU ...Sequence:
AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU GCGUAUUGAG AGAUACAAUU UGGGAAGAAA UUCCCAGAGU GUGUUUCUUU UGCGUUUAAC CUGAACAGUC UCAUCGUGGG CAUCUUGCGA UUCCAUUGGU GAGCAGCGAA GGAUUUGGUG GAUUACUAGC UAAUAGCAAU CUAUUUCAAA GAAUUCAAAC UUGGGGGAAU GCCUUGUUGA AUAGCCGGUC GCAAGACUGU GAUUCUUCAA GUGUAACCUC CUCUCAAAUC AGCGAUAUCA AACGUACCAU UCCGUGAAAC ACCGGGGUAU CUGUUUGGUG GAACCUGAUU AGAGGAAACU CAAAGAGUGC UAUGGUAUGG UGACGGAGUG CGCUGGUCAA GAGUGUAAAA GCUUUUUGAA CAGAGAGCAU UUCCGGCAGC AGAGAGACCU GAAAAAGCAA UUUUUCUGGA AUUUCAGCUG UUUCCAAACU CAAUAAGUAU CUUCUAGCAA GAGGGAAUAG GUGGGAAAAA AAAAAAGAGA UUUCGGUUUC UUUCUUUUUU ACUGCUUGUU GCUUCUUCUU UUAAGAUAGU
MassTheoretical: 225.543094 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: nucleic-acid, 18S pre-rRNA

nucleic acidName: 18S pre-rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAGAUAGUUA UCUGGUUGAU CCUGCCAGUA GUCAUAUGCU UGUCUCAAAG AUUAAGCCAU GCAUGUCUAA GUAUAAGCAA UUUAUACAGU GAAACUGCGA AUGGCUCAUU AAAUCAGUUA UCGUUUAUUU GAUAGUUCCU UUACUACAUG GUAUAACUGU GGUAAUUCUA ...Sequence:
AAGAUAGUUA UCUGGUUGAU CCUGCCAGUA GUCAUAUGCU UGUCUCAAAG AUUAAGCCAU GCAUGUCUAA GUAUAAGCAA UUUAUACAGU GAAACUGCGA AUGGCUCAUU AAAUCAGUUA UCGUUUAUUU GAUAGUUCCU UUACUACAUG GUAUAACUGU GGUAAUUCUA GAGCUAAUAC AUGCUUAAAA UCUCGACCCU UUGGAAGAGA UGUAUUUAUU AGAUAAAAAA UCAAUGUCUU CGGACUCUUU GAUGAUUCAU AAUAACUUUU CGAAUCGCAU GGCCUUGUGC UGGCGAUGGU UCAUUCAAAU UUCUGCCCUA UCAACUUUCG AUGGUAGGAU AGUGGCCUAC CAUGGUUUCA ACGGGUAACG GGGAAUAAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCAAUCCUAA UUCAGGGAGG UAGUGACAAU AAAUAACGAU ACAGGGCCCA UUCGGGUCUU GUAAUUGGAA UGAGUACAAU GUAAAUACCU UAACGAGGAA CAAUUGGAGG GCAAGUCUGG UGCCAGCAGC CGCGGUAAUU CCAGCUCCAA UAGCGUAUAU UAAAGUUGUU GCAGUUAAAA AGCUCGUAGU UGAACUUUGG GCCCGGUUGG CCGGUCCGAU UUUUUCGUGU ACUGGAUUUC CAACGGGGCC UUUCCUUCUG GCUAACCUUG AGUCCUUGUG GCUCUUGGCG AACCAGGACU UUUACUUUGA AAAAAUUAGA GUGUUCAAAG CAGGCGUAUU GCUCGAAUAU AUUAGCAUGG AAUAAUAGAA UAGGACGUUU GGUUCUAUUU UGUUGGUUUC UAGGACCAUC GUAAUGAUUA AUAGGGACGG UCGGGGGCAU CAGUAUUCAA UUGUCAGAGG UGAAAUUCUU GGAUUUAUUG AAGACUAACU ACUGCGAAAG CAUUUGCCAA GGACGUUUUC AUUAAUCAAG AACGAAAGUU AGGGGAUCGA AGAUGAUCAG AUACCGUCGU AGUCUUAACC AUAAACUAUG CCGACUAGGG AUCGGGUGGU GUUUUUUUAA UGACCCACUC GGCACCUUAC GAGAAAUCAA AGUCUUUGGG UUCUGGGGGG AGUAUGGUCG CAAGGCUGAA ACUUAAAGGA AUUGACGGAA GGGCACCACC AGGAGUGGAG CCUGCGGCUU AAUUUGACUC AACACGGGGA AACUCACCAG GUCCAGACAC AAUAAGGAUU GACAGAUUGA GAGCUCUUUC UUGAUUUUGU GGGUGGUGGU GCAUGGCCGU UCUUAGUUGG UGGAGUGAUU UGUCUGCUUA AUUGCGAUAA CGAACGAGAC CUUAACCUAC UAAAUAGUGG UGCUAGCAUU UGCUGGUUAU CCACUUCUUA GAGGGACUAU CGGUUUCAAG CCGAUGGAAG UUUGAGGCAA UAACAGGUCU GUGAUGCCCU UAGACGUUCU GGGCCGCACG CGCGCUACAC UGACGGAGCC AGCGAGUCUA ACCUUGGCCG AGAGGUCUUG GUAAUCUUGU GAAACUCCGU CGUGCUGGGG AUAGAGCAUU GUAAUUAUUG CUCUUCAACG AGGAAUUCCU AGUAAGCGCA AGUCAUCAGC UUGCGUUGAU UACGUCCCUG CCCUUUGUAC ACACCGCCCG UCGCUAGUAC CGAUUGAAUG GCUUAGUGAG GCCUCAGGAU CUGCUUAGAG AAGGGGGCAA CUCCAUCUCA GAGCGGAGAA UUUGGACAAA CUUGGUCAUU UAGAGGAACU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA
MassTheoretical: 582.381688 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.488631 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, 40S ribosomal protein S14-A

ProteinName: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.071641 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, 40S ribosomal protein S22-B

ProteinName: 40S ribosomal protein S22-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, rRNA 2'-O-methyltransferase fibrillarin

ProteinName: rRNA 2'-O-methyltransferase fibrillarin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, Nucleolar protein 56

ProteinName: Nucleolar protein 56Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.961152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #23: protein, Nucleolar protein 58

ProteinName: Nucleolar protein 58Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.060344 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #24: protein, Ribosomal RNA-processing protein 9

ProteinName: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #25: protein, 13 kDa ribonucleoprotein-associated protein

ProteinName: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #26: protein, U3 small nucleolar RNA-associated protein 4

ProteinName: U3 small nucleolar RNA-associated protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.909242 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #27: protein, U3 small nucleolar RNA-associated protein 5

ProteinName: U3 small nucleolar RNA-associated protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #28: protein, U3 small nucleolar RNA-associated protein 8

ProteinName: U3 small nucleolar RNA-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.269648 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #29: protein, U3 small nucleolar RNA-associated protein 9

ProteinName: U3 small nucleolar RNA-associated protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.347254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #30: protein, U3 small nucleolar RNA-associated protein 10

ProteinName: U3 small nucleolar RNA-associated protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 200.298984 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #31: protein, U3 small nucleolar RNA-associated protein 15

ProteinName: U3 small nucleolar RNA-associated protein 15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #32: protein, NET1-associated nuclear protein 1

ProteinName: NET1-associated nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.341734 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #33: protein, Periodic tryptophan protein 2

ProteinName: Periodic tryptophan protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #34: protein, U3 small nucleolar RNA-associated protein 12

ProteinName: U3 small nucleolar RNA-associated protein 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.481133 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #35: protein, U3 small nucleolar RNA-associated protein 13

ProteinName: U3 small nucleolar RNA-associated protein 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.132562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #36: protein, U3 small nucleolar RNA-associated protein 18

ProteinName: U3 small nucleolar RNA-associated protein 18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #37: protein, U3 small nucleolar RNA-associated protein 21

ProteinName: U3 small nucleolar RNA-associated protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #38: protein, U3 small nucleolar RNA-associated protein 6

ProteinName: U3 small nucleolar RNA-associated protein 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.495277 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #39: protein, Bud site selection protein 21

ProteinName: Bud site selection protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.431016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #40: protein, U3 small nucleolar RNA-associated protein 7

ProteinName: U3 small nucleolar RNA-associated protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #41: protein, U3 small nucleolar RNA-associated protein 11

ProteinName: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #42: protein, U3 small nucleolar RNA-associated protein MPP10

ProteinName: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #43: protein, U3 small nucleolar ribonucleoprotein protein IMP3

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #44: protein, U3 small nucleolar ribonucleoprotein protein IMP4

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #45: protein, Something about silencing protein 10

ProteinName: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.364398 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #46: protein, Protein SOF1

ProteinName: Protein SOF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #47: protein, rRNA-processing protein FCF2

ProteinName: rRNA-processing protein FCF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #48: protein, rRNA-processing protein FCF1

ProteinName: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #49: protein, Ribosome biogenesis protein ENP2

ProteinName: Ribosome biogenesis protein ENP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.864172 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #50: protein, U3 small nucleolar ribonucleoprotein protein LCP5

ProteinName: U3 small nucleolar ribonucleoprotein protein LCP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.864391 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #51: protein, KRR1 small subunit processome component

ProteinName: KRR1 small subunit processome component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #52: protein, rRNA biogenesis protein RRP5

ProteinName: rRNA biogenesis protein RRP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 193.411422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #53: protein, U3 small nucleolar RNA-associated protein 22

ProteinName: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #54: protein, Ribosomal RNA-processing protein 7

ProteinName: Ribosomal RNA-processing protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #55: protein, Ribosomal RNA small subunit methyltransferase NEP1

ProteinName: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #56: protein, Ribosome biogenesis protein UTP30

ProteinName: Ribosome biogenesis protein UTP30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #57: protein, Ribosome biogenesis protein BMS1

ProteinName: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.792281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #58: protein, RNA 3'-terminal phosphate cyclase-like protein

ProteinName: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #59: protein, RNA cytidine acetyltransferase

ProteinName: RNA cytidine acetyltransferase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 119.509445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #60: protein, Nucleolar complex protein 14

ProteinName: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.463195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #61: protein, Nucleolar complex protein 4

ProteinName: Nucleolar complex protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.707844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #62: protein, U3 small nucleolar RNA-associated protein 20

ProteinName: U3 small nucleolar RNA-associated protein 20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 287.9155 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #63: protein, U3 small nucleolar RNA-associated protein 14

ProteinName: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.18975 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #64: protein, Essential nuclear protein 1

ProteinName: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #65: protein, Pno1

ProteinName: Pno1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.356477 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #66: protein, Protein FAF1

ProteinName: Protein FAF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.961512 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #67: protein, Regulator of rDNA transcription protein 14

ProteinName: Regulator of rDNA transcription protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.898289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #68: protein, Protein BFR2

ProteinName: Protein BFR2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.285039 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #69: protein, Unassigned helices

ProteinName: Unassigned helices / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.549291 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #70: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #71: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #72: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 18028

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 26582
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution Method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Input PDB model: 6LQP
Output model

+
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