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- EMDB-8473: Architecture of the yeast small subunit processome -

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Basic information

Entry
Database: EMDB / ID: EMD-8473
TitleArchitecture of the yeast small subunit processome
Map data
SampleSmall subunit processome
  • (nucleic-acidNucleic acid) x 6
  • rpS6_ES6
  • rpS4_ES4
  • rpS5_US7
  • rpS7_eS7
  • rpS8_eS8
  • rpS9_uS4
  • rpS16_uS9
  • rpS11_uS17
  • rpS22_uS8
  • rpS24_eS24
  • rpS28_eS28
  • Utp4
  • UtpA_CTD1
  • UtpA_CTD2
  • (Beta-propeller ...) x 3
  • Utp17
  • Utp1
  • Utp6
  • Utp12
  • Utp13
  • Utp18
  • Utp21
  • Enp2
  • UtpA_CTD4
  • (Kre33) x 2
  • Imp3
  • Nop56
  • Nop58
  • (Nop1) x 2
  • Snu13NHP2L1
  • Ribosomal RNA-processing protein 9
  • RNA 3'-terminal phosphate cyclase-like protein
  • Bms1,Ribosome biogenesis protein BMS1,Bms1
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Utp24
  • Imp4
  • Utp30
  • Unassigned KH domain
  • Utp20
  • (Repeat protein ...) x 2
  • 40S ribosomal protein S23-ARibosome
  • Unassigned protein helices
Function / homology
Function and homology information


Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex ...Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / rRNA base methylation / U4 snRNA binding / U3 snoRNA binding / rRNA export from nucleus / precatalytic spliceosome / 90S preribosome / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA 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 / regulation of translational fidelity / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / maturation of LSU-rRNA / endoribonuclease activity / maintenance of translational fidelity / 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) / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Ribosomal protein S4/S9, eukaryotic/archaeal / AARP2CN / Ribosomal protein S5/S7 / RNA 3'-terminal phosphate cyclase / Small-subunit processome, Utp21 / Quinoprotein alcohol dehydrogenase-like superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S28e ...Ribosomal protein S4/S9, eukaryotic/archaeal / AARP2CN / Ribosomal protein S5/S7 / RNA 3'-terminal phosphate cyclase / Small-subunit processome, Utp21 / Quinoprotein alcohol dehydrogenase-like superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S28e / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S17/S11 / Ribosomal protein S7e / Ribosomal protein S12/S23 / RNA-binding S4 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae conserved site / ATPase, AAA-type, core / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Ribosomal protein S8 / Ribosomal protein S24e / Ribosomal protein S4/S9, N-terminal / WD40 repeat / Ribosomal protein S6e / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Alpha/beta knot methyltransferases / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S28e conserved site / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / Ribosomal protein S4, KOW domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Anaphase-promoting complex subunit 4, WD40 domain / KOW
40S ribosomal protein S5 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / 13 kDa ribonucleoprotein-associated protein / 40S ribosomal protein S7-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A ...40S ribosomal protein S5 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / 13 kDa ribonucleoprotein-associated protein / 40S ribosomal protein S7-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S22-A / 40S ribosomal protein S9-A / 40S ribosomal protein S28-A
Biological speciesSaccharomyces cerevisiae S288c (yeast) / yeast (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsChaker-Margot M / Barandun J / Hunziker M / Klinge S
CitationJournal: Science / Year: 2017
Title: Architecture of the yeast small subunit processome.
Authors: Malik Chaker-Margot / Jonas Barandun / Mirjam Hunziker / Sebastian Klinge /
Abstract: The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of ...The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionNov 22, 2016-
Header (metadata) releaseDec 21, 2016-
Map releaseDec 21, 2016-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5tzs
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8473.png

Downloads & links

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Map

FileDownload / File: emd_8473.map.gz / Format: CCP4 / Size: 209.3 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 380 pix.
= 503.5 Å		1.33 Å/pix.
x 380 pix.
= 503.5 Å		1.33 Å/pix.
x 380 pix.
= 503.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.043499846 - 0.085774556
Average (Standard dev.)0.00048635554 (±0.003368933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 503.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3251.3251.325
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z503.500503.500503.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0430.0860.000

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Supplemental data

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Sample components

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Entire Small subunit processome

EntireName: Small subunit processome / Number of components: 54

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Component #1: protein, Small subunit processome

ProteinName: Small subunit processome / Recombinant expression: No
MassTheoretical: 4 MDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: nucleic-acid, 5' external transcribed spacer

nucleic acidName: 5' external transcribed spacer / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNGGAUU ...Sequence:
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNGGAUU UGGUGGNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNN
MassTheoretical: 72.801469 kDa
SourceSpecies: yeast (fungus)

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Component #3: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ...Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUUCGU GUACUGGAUU UCCAACGGGG CCUUUCCUUC UGGCUAACCU UGAGUCCUUG UGGCUCUUGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUGUUCAA AGCAGGCGUA UUGCUCGAAU AUAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUUC AAUUGUCAGA GGUGAAAUUC UUGGAUUUAU UGAAGACUAA CUACUGCGAA AGCAUUUGCC AAGGACGUUU UCAUUAAUCA AGAACGAAAG UUAGGGGAUC GAAGAUGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGACUAG GGAUCGGGUG GUGUUUUUUU AAUGACCCAC UCGGCACCUU ACGAGAAAUC AAAGUCUUUG GGUUCUGGGG GGAGUAUGGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG AGCCUGCGGC UUAAUUUGAC UCAACACGGG GAAACUCACC AGGUCCAGAC ACAAUAAGGA UUGACAGAUU GAGAGCUCUU UCUUGAUUUU GUGGGUGGUG GUGCAUGGCC GUUCUUAGUU GGUGGAGUGA UUUGUCUGCU UAAUUGCGAU AACGAACGAG ACCUUAACCU ACUAAAUAGU GGUGCUAGCA UUUGCUGGUU AUCCACUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUC UAACCUUGGC CGAGAGGUCU UGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGGAG AAUUUGGACA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA
MassTheoretical: 579.761938 kDa
SourceSpecies: yeast (fungus)

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Component #4: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
NNNNNNNNNN NNNNNNNNNN NNNCCACUGA AUCCAACUUG GUUGAUGAGU UAACCUUUGU ACCCGUGAGA AACCGUAUGG CCGAUGAUCU UACCCAUGGG UGGGUACAAA UGGCAGUCUG ACAAGU
MassTheoretical: 37.614797 kDa
SourceSpecies: yeast (fungus)

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Component #5: protein, rpS6_ES6

ProteinName: rpS6_ES6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: yeast (fungus)

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Component #6: protein, rpS4_ES4

ProteinName: rpS4_ES4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: yeast (fungus)

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Component #7: protein, rpS5_US7

ProteinName: rpS5_US7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: yeast (fungus)

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Component #8: protein, rpS7_eS7

ProteinName: rpS7_eS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: yeast (fungus)

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Component #9: protein, rpS8_eS8

ProteinName: rpS8_eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: yeast (fungus)

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Component #10: protein, rpS9_uS4

ProteinName: rpS9_uS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: yeast (fungus)

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Component #11: nucleic-acid, 5' domain-associated

nucleic acidName: 5' domain-associated / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNN
MassTheoretical: 7.602739 kDa
SourceSpecies: yeast (fungus)

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Component #12: nucleic-acid, 3' domain-associated

nucleic acidName: 3' domain-associated / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNN
MassTheoretical: 21.133273 kDa
SourceSpecies: yeast (fungus)

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Component #13: protein, rpS16_uS9

ProteinName: rpS16_uS9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: yeast (fungus)

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Component #14: protein, rpS11_uS17

ProteinName: rpS11_uS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: yeast (fungus)

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Component #15: protein, rpS22_uS8

ProteinName: rpS22_uS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: yeast (fungus)

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Component #16: protein, rpS24_eS24

ProteinName: rpS24_eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: yeast (fungus)

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Component #17: protein, rpS28_eS28

ProteinName: rpS28_eS28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.619874 kDa
SourceSpecies: yeast (fungus)

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Component #18: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.315152 kDa
SourceSpecies: yeast (fungus)

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Component #19: protein, UtpA_CTD1

ProteinName: UtpA_CTD1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.996461 kDa
SourceSpecies: yeast (fungus)

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Component #20: protein, UtpA_CTD2

ProteinName: UtpA_CTD2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.124238 kDa
SourceSpecies: yeast (fungus)

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Component #21: protein, Beta-propeller 2

ProteinName: Beta-propeller 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.974984 kDa
SourceSpecies: yeast (fungus)

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Component #22: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.400258 kDa
SourceSpecies: yeast (fungus)

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Component #23: protein, Utp1

ProteinName: Utp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.315098 kDa
SourceSpecies: yeast (fungus)

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Component #24: protein, Utp6

ProteinName: Utp6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.059973 kDa
SourceSpecies: yeast (fungus)

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Component #25: protein, Utp12

ProteinName: Utp12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.442441 kDa
SourceSpecies: yeast (fungus)

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Component #26: protein, Utp13

ProteinName: Utp13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.038156 kDa
SourceSpecies: yeast (fungus)

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Component #27: protein, Utp18

ProteinName: Utp18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.294152 kDa
SourceSpecies: yeast (fungus)

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Component #28: protein, Utp21

ProteinName: Utp21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.438234 kDa
SourceSpecies: yeast (fungus)

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Component #29: protein, Beta-propeller 5

ProteinName: Beta-propeller 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.187688 kDa
SourceSpecies: yeast (fungus)

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Component #30: protein, Enp2

ProteinName: Enp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.400504 kDa
SourceSpecies: yeast (fungus)

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Component #31: protein, UtpA_CTD4

ProteinName: UtpA_CTD4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.868924 kDa
SourceSpecies: yeast (fungus)

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Component #32: protein, Kre33

ProteinName: Kre33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.485305 kDa
SourceSpecies: yeast (fungus)

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Component #33: protein, Kre33

ProteinName: Kre33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.570406 kDa
SourceSpecies: yeast (fungus)

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Component #34: protein, Imp3

ProteinName: Imp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.868854 kDa
SourceSpecies: yeast (fungus)

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Component #35: protein, Nop56

ProteinName: Nop56 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.570598 kDa
SourceSpecies: yeast (fungus)

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Component #36: protein, Nop58

ProteinName: Nop58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.038656 kDa
SourceSpecies: yeast (fungus)

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Component #37: protein, Nop1

ProteinName: Nop1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.826139 kDa
SourceSpecies: yeast (fungus)

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Component #38: protein, Nop1

ProteinName: Nop1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.400619 kDa
SourceSpecies: yeast (fungus)

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Component #39: protein, Snu13

ProteinName: Snu13NHP2L1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: yeast (fungus)

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Component #40: protein, Ribosomal RNA-processing protein 9

ProteinName: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: yeast (fungus)

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Component #41: 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: yeast (fungus)

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Component #42: protein, Bms1,Ribosome biogenesis protein BMS1,Bms1

ProteinName: Bms1,Ribosome biogenesis protein BMS1,Bms1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.598305 kDa
SourceSpecies: yeast (fungus)

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Component #43: 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: yeast (fungus)

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Component #44: protein, Utp24

ProteinName: Utp24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.571022 kDa
SourceSpecies: yeast (fungus)

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Component #45: protein, Imp4

ProteinName: Imp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.29438 kDa
SourceSpecies: yeast (fungus)

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Component #46: protein, Utp30

ProteinName: Utp30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.634798 kDa
SourceSpecies: yeast (fungus)

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Component #47: protein, Unassigned KH domain

ProteinName: Unassigned KH domain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.911357 kDa
SourceSpecies: yeast (fungus)

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Component #48: protein, Utp20

ProteinName: Utp20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 78.654266 kDa
SourceSpecies: yeast (fungus)

+
Component #49: protein, Repeat protein 2

ProteinName: Repeat protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.676939 kDa
SourceSpecies: yeast (fungus)

+
Component #50: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: yeast (fungus)

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Component #51: protein, Beta-propeller 1

ProteinName: Beta-propeller 1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.698311 kDa
SourceSpecies: yeast (fungus)

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Component #52: protein, Repeat protein 1

ProteinName: Repeat protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.378965 kDa
SourceSpecies: yeast (fungus)

+
Component #53: protein, Unassigned protein helices

ProteinName: Unassigned protein helices / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.166234 kDa
SourceSpecies: yeast (fungus)

+
Component #54: nucleic-acid, Unassigned RNA helices

nucleic acidName: Unassigned RNA helices / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNN
MassTheoretical: 14.85826 kDa
SourceSpecies: yeast (fungus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/mL / pH: 7.7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing..

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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. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600.0 - 2600.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (78.0 - 80.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1714

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 33813
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 300
Output model

5tzs

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