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- EMDB-8859: The complete structure of the small subunit processome -

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Basic information

Entry
Database: EMDB / ID: EMD-8859
TitleThe complete structure of the small subunit processome
Map data
SampleSmall subunit processome:
(nucleic-acidNucleic acid) x 3 / rpS18_uS13 / rpS4_eS4 / rpS5_uS7 / rpS6_eS6 / rpS7_eS7 / rpS8_eS8 / rpS9_uS4 / rpS16_uS9 / rpS11_uS17 ...(nucleic-acidNucleic acid) x 3 / rpS18_uS13 / rpS4_eS4 / rpS5_uS7 / rpS6_eS6 / rpS7_eS7 / rpS8_eS8 / rpS9_uS4 / rpS16_uS9 / rpS11_uS17 / rpS22_uS8 / rpS24_eS24 / rpS28_eS28 / Utp17 / Utp8 / Utp15 / Utp9 / Utp5 / Utp10 / Utp4 / Utp1 / Utp6 / Utp12 / Utp13 / Utp18 / Utp21 / Sof1 / Enp2 / Utp7 / Kre33 / Imp3 / Mpp10 / Sas10SAS (TV station) / Lcp5 / Bud21 / Faf1 / rpS13_uS15 / rpS14_uS11 / Utp22 / Rrp7 / Rrp5 / Krr1 / Nop56 / Nop58 / Nop1 / Snu13NHP2L1 / Rrp9 / Rcl1 / Bms1 / Emg1 / Utp24 / Imp4 / Utp30 / Pno1 / Utp20 / Fcf2 / rpS23_uS12 / Utp14 / Nop14 / Noc4 / Rrt14 / Unassigned peptides / Utp11 / Enp1 / ligand
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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome ...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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / 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 / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / rDNA heterochromatin / 90S preribosome assembly / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / small nuclear ribonucleoprotein complex / histone glutamine methylation / U4 snRNA binding / 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 / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / positive regulation of translational fidelity / enzyme activator activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / cell cycle / translation / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
NOP5, N-terminal / NOSIC / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / NUC153 / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily ...NOP5, N-terminal / NOSIC / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / NUC153 / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal domain / BP28, C-terminal domain / U3 snoRNA associated / S15/NS1, RNA-binding / 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 / Small-subunit processome, Utp13 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S13-like, H2TH / Bystin / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal protein S4/S9, eukaryotic/archaeal / RNA-binding S4 domain / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / NOL6/Upt22 / CCAAT-binding factor / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Helicase domain / KOW / Ribosomal protein S12/S23 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Nucleolar protein 14 / Sof1-like protein / Small-subunit processome, Utp21 / Armadillo-type fold / WD40-repeat-containing domain / Nop domain / PIN-like domain superfamily / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal RNA-processing protein 7, C-terminal domain / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Regulator of rDNA transcription 14 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA assembly KRR1 / Ribosomal protein S4, conserved site / G-protein beta WD-40 repeat / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / U3 small nucleolar RNA-associated protein 8 / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / WD40 repeat, conserved site
NET1-associated nuclear protein 1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 8 ...NET1-associated nuclear protein 1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 8 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 12 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 10 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Nucleolar complex protein 14 / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S7-A / Protein FAF1 / 40S ribosomal protein S11-A / 40S ribosomal protein S5 / KRR1 small subunit processome component / Regulator of rDNA transcription 14 / U3 small nucleolar RNA-associated protein 11 / Regulator of rDNA transcription 14 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S16-A / U3 small nucleolar RNA-associated protein 18 / 40S ribosomal protein S18-A / 40S ribosomal protein S23-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / Periodic tryptophan protein 2 / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / 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 / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae BY4741 (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBarandun J / Chaker-Margot M / Hunziker M / Klinge S
Funding support United States, Switzerland, European Union, France, Canada, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
European Molecular Biology Organization (EMBO)ALTF 51-2014European Union
Human Frontier Science Program (HFSP) France
Natural Sciences and Engineering Research Council (NSERC, Canada)PGS-D Canada
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: The complete structure of the small-subunit processome.
Authors: Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge /
Abstract: The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit ...The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 26, 2017-
Header (metadata) releaseSep 13, 2017-
Map releaseSep 27, 2017-
UpdateJan 1, 2020-
Current statusJan 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wlc
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8859.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 400 pix.
= 520. Å
1.3 Å/pix.
x 400 pix.
= 520. Å
1.3 Å/pix.
x 400 pix.
= 520. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.10548593 - 0.16638078
Average (Standard dev.)0.00023483255 (±0.005812679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 520.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1050.1660.000

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Supplemental data

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Additional map: small subunit processome, central domain map

Fileemd_8859_additional_1.map
Annotationsmall subunit processome, central domain map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: small subunit processome, core map

Fileemd_8859_additional_2.map
Annotationsmall subunit processome, core map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: small subunit processome, overall map 2

Fileemd_8859_additional_3.map
Annotationsmall subunit processome, overall map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: small subunit processome, 3' domain map

Fileemd_8859_additional_4.map
Annotationsmall subunit processome, 3' domain map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Small subunit processome

EntireName: Small subunit processome / Number of components: 68

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Component #1: protein, Small subunit processome

ProteinName: Small subunit processome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast)

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Component #2: 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: BY4741

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Component #3: nucleic-acid, 18S pre-rRNA

nucleic acidName: 18S pre-rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AGAUAGUUAU CUGGUUGAUC CUGCCAGUAG UCAUAUGCUU GUCUCAAAGA UUAAGCCAUG CAUGUCUAAG UAUAAGCAAU UUAUACAGUG AAACUGCGAA UGGCUCAUUA AAUCAGUUAU CGUUUAUUUG AUAGUUCCUU UACUACAUGG UAUAACUGUG GUAAUUCUAG ...Sequence:
AGAUAGUUAU CUGGUUGAUC CUGCCAGUAG UCAUAUGCUU GUCUCAAAGA UUAAGCCAUG CAUGUCUAAG UAUAAGCAAU UUAUACAGUG AAACUGCGAA UGGCUCAUUA AAUCAGUUAU CGUUUAUUUG AUAGUUCCUU UACUACAUGG UAUAACUGUG GUAAUUCUAG AGCUAAUACA UGCUUAAAAU CUCGACCCUU UGGAAGAGAU GUAUUUAUUA GAUAAAAAAU CAAUGUCUUC GGACUCUUUG AUGAUUCAUA AUAACUUUUC GAAUCGCAUG GCCUUGUGCU GGCGAUGGUU CAUUCAAAUU UCUGCCCUAU CAACUUUCGA UGGUAGGAUA GUGGCCUACC AUGGUUUCAA CGGGUAACGG GGAAUAAGGG UUCGAUUCCG GAGAGGGAGC CUGAGAAACG GCUACCACAU CCAAGGAAGG CAGCAGGCGC GCAAAUUACC CAAUCCUAAU UCAGGGAGGU AGUGACAAUA AAUAACGAUA CAGGGCCCAU UCGGGUCUUG UAAUUGGAAU GAGUACAAUG UAAAUACCUU AACGAGGAAC AAUUGGAGGG CAAGUCUGGU GCCAGCAGCC GCGGUAAUUC CAGCUCCAAU AGCGUAUAUU AAAGUUGUUG CAGUUAAAAA GCUCGUAGUU GAACUUUGGG CCCGGUUGGC CGGUCCGAUU UUUUCGUGUA CUGGAUUUCC AACGGGGCCU UUCCUUCUGG CUAACCUUGA GUCCUUGUGG CUCUUGGCGA ACCAGGACUU UUACUUUGAA AAAAUUAGAG UGUUCAAAGC AGGCGUAUUG CUCGAAUAUA UUAGCAUGGA AUAAUAGAAU AGGACGUUUG GUUCUAUUUU GUUGGUUUCU AGGACCAUCG UAAUGAUUAA UAGGGACGGU CGGGGGCAUC AGUAUUCAAU UGUCAGAGGU GAAAUUCUUG GAUUUAUUGA AGACUAACUA CUGCGAAAGC AUUUGCCAAG GACGUUUUCA UUAAUCAAGA ACGAAAGUUA GGGGAUCGAA GAUGAUCAGA UACCGUCGUA GUCUUAACCA UAAACUAUGC CGACUAGGGA UCGGGUGGUG UUUUUUUAAU GACCCACUCG GCACCUUACG AGAAAUCAAA GUCUUUGGGU UCUGGGGGGA GUAUGGUCGC AAGGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGGAA ACUCACCAGG UCCAGACACA AUAAGGAUUG ACAGAUUGAG AGCUCUUUCU UGAUUUUGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGUGAUUU GUCUGCUUAA UUGCGAUAAC GAACGAGACC UUAACCUACU AAAUAGUGGU GCUAGCAUUU GCUGGUUAUC CACUUCUUAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UUGAGGCAAU AACAGGUCUG UGAUGCCCUU AGACGUUCUG GGCCGCACGC GCGCUACACU GACGGAGCCA GCGAGUCUAA CCUUGGCCGA GAGGUCUUGG UAAUCUUGUG AAACUCCGUC GUGCUGGGGA UAGAGCAUUG UAAUUAUUGC UCUUCAACGA GGAAUUCCUA GUAAGCGCAA GUCAUCAGCU UGCGUUGAUU ACGUCCCUGC CCUUUGUACA CACCGCCCGU CGCUAGUACC GAUUGAAUGG CUUAGUGAGG CCUCAGGAUC UGCUUAGAGA AGGGGGCAAC UCCAUCUCAG AGCGGAGAAU UUGGACAAAC UUGGUCAUUU AGAGGAACUA AAAGUCGUAA CAAGGUUUCC GUAGGUGAAC CUGCGGAAGG AUCAUUA
MassTheoretical: 582.052438 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #4: 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: BY4741

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Component #5: protein, rpS18_uS13

ProteinName: rpS18_uS13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.773332 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #6: protein, rpS4_eS4

ProteinName: rpS4_eS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #7: protein, rpS5_uS7

ProteinName: rpS5_uS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #8: protein, rpS6_eS6

ProteinName: rpS6_eS6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #9: protein, rpS7_eS7

ProteinName: rpS7_eS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #10: protein, rpS8_eS8

ProteinName: rpS8_eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #11: protein, rpS9_uS4

ProteinName: rpS9_uS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #12: protein, rpS16_uS9

ProteinName: rpS16_uS9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #13: protein, rpS11_uS17

ProteinName: rpS11_uS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #14: protein, rpS22_uS8

ProteinName: rpS22_uS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #15: protein, rpS24_eS24

ProteinName: rpS24_eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #16: protein, rpS28_eS28

ProteinName: rpS28_eS28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #17: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.960445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #18: protein, Utp8

ProteinName: Utp8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.572977 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #19: protein, Utp15

ProteinName: Utp15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

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Component #20: protein, Utp9

ProteinName: Utp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.378512 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #21: protein, Utp5

ProteinName: Utp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #22: protein, Utp10

ProteinName: Utp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 200.020719 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #23: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.3165 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #24: protein, Utp1

ProteinName: Utp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #25: protein, Utp6

ProteinName: Utp6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.437402 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #26: protein, Utp12

ProteinName: Utp12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.037648 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #27: protein, Utp13

ProteinName: Utp13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.035867 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #28: protein, Utp18

ProteinName: Utp18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #29: protein, Utp21

ProteinName: Utp21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #30: protein, Sof1

ProteinName: Sof1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #31: protein, Enp2

ProteinName: Enp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.864172 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #32: protein, Utp7

ProteinName: Utp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #33: protein, Kre33

ProteinName: Kre33 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 95.337062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #34: protein, Imp3

ProteinName: Imp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #35: protein, Mpp10

ProteinName: Mpp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #36: protein, Sas10

ProteinName: Sas10SAS (TV station) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.705703 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #37: protein, Lcp5

ProteinName: Lcp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.864391 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #38: protein, Bud21

ProteinName: Bud21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.835627 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #39: protein, Faf1

ProteinName: Faf1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.173699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #40: protein, rpS13_uS15

ProteinName: rpS13_uS15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #41: protein, rpS14_uS11

ProteinName: rpS14_uS11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #42: protein, Utp22

ProteinName: Utp22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #43: protein, Rrp7

ProteinName: Rrp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #44: protein, Rrp5

ProteinName: Rrp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 193.411422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #45: protein, Krr1

ProteinName: Krr1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #46: protein, Nop56

ProteinName: Nop56 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.394863 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #47: protein, Nop58

ProteinName: Nop58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.81452 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #48: protein, Nop1

ProteinName: Nop1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #49: protein, Snu13

ProteinName: Snu13NHP2L1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #50: protein, Rrp9

ProteinName: Rrp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #51: protein, Rcl1

ProteinName: Rcl1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #52: protein, Bms1

ProteinName: Bms1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.152938 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #53: protein, Emg1

ProteinName: Emg1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #54: protein, Utp24

ProteinName: Utp24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #55: protein, Imp4

ProteinName: Imp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #56: protein, Utp30

ProteinName: Utp30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #57: protein, Pno1

ProteinName: Pno1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #58: protein, Utp20

ProteinName: Utp20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.59018 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #59: protein, Fcf2

ProteinName: Fcf2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #60: protein, rpS23_uS12

ProteinName: rpS23_uS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #61: protein, Utp14

ProteinName: Utp14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.101461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #62: protein, Nop14

ProteinName: Nop14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.993961 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #63: protein, Noc4

ProteinName: Noc4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.369125 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #64: protein, Rrt14

ProteinName: Rrt14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.036877 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #65: protein, Unassigned peptides

ProteinName: Unassigned peptides / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.783818 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #66: protein, Utp11

ProteinName: Utp11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #67: protein, Enp1

ProteinName: Enp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BY4741

+
Component #68: ligand, ZINC ION

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

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/mL / pH: 7.7
Support film50 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 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: 1.56 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600.0 - 2600.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 10029

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 284213
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 338.9
Output model

+
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