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- EMDB-10842: pre-60S State NE2 (TAP-Flag-Nop53) -

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Basic information

Entry
Database: EMDB / ID: EMD-10842
Titlepre-60S State NE2 (TAP-Flag-Nop53)
Map data
Samplepre-60S assembly state NE2
  • (60S ribosomal protein ...) x 33
  • Nucleolar GTP-binding protein 1
  • Bud site selection protein 20
  • (Ribosome biogenesis protein ...) x 5
  • Ribosome assembly factor MRT4
  • Eukaryotic translation initiation factor 6
  • UPF0642 protein YBL028C
  • (nucleic-acidNucleic acid) x 3
  • Proteasome-interacting protein CIC1
  • Pescadillo homolog
  • Nuclear GTP-binding protein NUG1
  • ligand
Function / homology
Function and homology information


exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / positive regulation of ATPase activity / ribosomal large subunit binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding ...exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / positive regulation of ATPase activity / ribosomal large subunit binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / ATPase activator activity / ribosomal subunit export from nucleus / 90S preribosome / preribosome, large subunit precursor / ribonucleoprotein complex assembly / proteasome binding / negative regulation of mRNA splicing, via spliceosome / regulation of translational fidelity / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / proteasome complex / mature ribosome assembly / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / protein catabolic process / protein-macromolecule adaptor activity / rRNA processing / large ribosomal subunit rRNA binding / macroautophagy / cytoplasmic translation / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / ribosome binding / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / ATPase binding / nucleic acid binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L25/L23 / Zinc finger C2H2-type / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Guanine nucleotide-binding protein-like 3, N-terminal domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich ...Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L25/L23 / Zinc finger C2H2-type / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Guanine nucleotide-binding protein-like 3, N-terminal domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L29, conserved site / Ribosomal protein L30, N-terminal / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Uncharacterised protein family UPF0642 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / NOG, C-terminal / Ribosomal protein L14P, conserved site / Ribosomal protein L34Ae / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L13 / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L7, eukaryotic / GTP binding domain / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Translation protein, beta-barrel domain superfamily / Pescadillo / Nucleolar GTP-binding protein 1, Rossman-fold domain / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Ribosome biogenesis protein Nop53/GLTSCR2 / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L3, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosome assembly factor Mrt4 / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L19/L19e superfamily / RNA-binding domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / BRCT domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Nucleolar GTP-binding protein 1 / Ribosomal protein L31e, conserved site / Zinc finger, double-stranded RNA binding / Ribosomal protein L39e, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L15e core domain superfamily / Ribosomal protein L30, central domain, archaeal type / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1-like / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L7Ae conserved site / Ribosomal protein L13 superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L31e / Ribosomal protein L18e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily
60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / UPF0642 protein YBL028C / Proteasome-interacting protein CIC1 / Nuclear GTP-binding protein NUG1 / Ribosome biogenesis protein RLP7 / Ribosome biogenesis protein RLP24 ...60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosome assembly factor MRT4 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / UPF0642 protein YBL028C / Proteasome-interacting protein CIC1 / Nuclear GTP-binding protein NUG1 / Ribosome biogenesis protein RLP7 / Ribosome biogenesis protein RLP24 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / Ribosome biogenesis protein 15 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Bud site selection protein 20 / Ribosome biogenesis protein NOP53 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L30 / 60S ribosomal protein L3 / 60S ribosomal protein L15-A / 60S ribosomal protein L4-A / 60S ribosomal protein L33-A / Ribosome biogenesis protein NSA2 / Pescadillo homolog / 60S ribosomal protein L28 / 60S ribosomal protein L25 / 60S ribosomal protein L39 / 60S ribosomal protein L7-A / 60S ribosomal protein L9-A / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L36-A / 60S ribosomal protein L35-A / 60S ribosomal protein L22-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 60S ribosomal protein L23-A / 60S ribosomal protein L2-A / 60S ribosomal protein L18-A / 60S ribosomal protein L19-A / 60S ribosomal protein L13-A
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKater L / Beckmann R
CitationJournal: Mol. Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
Validation ReportPDB-ID: 6yly

SummaryFull reportAbout validation report
History
DepositionApr 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yly
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10842.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 416.256 Å
1.08 Å/pix.
x 384 pix.
= 416.256 Å
1.08 Å/pix.
x 384 pix.
= 416.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.35170728 - 0.57454145
Average (Standard dev.)-0.00013341429 (±0.014125629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 416.25598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z416.256416.256416.256
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.3520.575-0.000

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Supplemental data

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10842_half_map_1.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10842_half_map_2.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire pre-60S assembly state NE2

EntireName: pre-60S assembly state NE2 / Details: TAP-Flag-Nop53 derived pre-60S assembly complex / Number of components: 51

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Component #1: protein, pre-60S assembly state NE2

ProteinName: pre-60S assembly state NE2 / Details: TAP-Flag-Nop53 derived pre-60S assembly complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.463574 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.761666 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.850793 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Nucleolar GTP-binding protein 1

ProteinName: Nucleolar GTP-binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.531227 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.159125 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.430364 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.980158 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.809441 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.686281 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.17713 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.17582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.673196 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, Bud site selection protein 20

ProteinName: Bud site selection protein 20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.546982 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.94264 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.151259 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.877395 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.845561 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.604164 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.35864 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.195066 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.112952 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.482357 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, Ribosome biogenesis protein RLP24

ProteinName: Ribosome biogenesis protein RLP24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.02765 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.247227 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.609252 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #30: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.762316 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #31: protein, Ribosome biogenesis protein NSA2

ProteinName: Ribosome biogenesis protein NSA2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.786783 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #32: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #33: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.279266 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #34: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.711359 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #35: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.49395 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #36: protein, Ribosome assembly factor MRT4

ProteinName: Ribosome assembly factor MRT4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.098012 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #37: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.787612 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #38: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.265784 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #39: protein, Eukaryotic translation initiation factor 6

ProteinName: Eukaryotic translation initiation factor 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.476605 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #40: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.56836 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #41: protein, UPF0642 protein YBL028C

ProteinName: UPF0642 protein YBL028C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.435429 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #42: nucleic-acid, 25S rRNA

nucleic acidName: 25S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG ...Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #43: nucleic-acid, 5.8S rRNA

nucleic acidName: 5.8S rRNA5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUUU
MassTheoretical: 50.682922 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #44: protein, Proteasome-interacting protein CIC1

ProteinName: Proteasome-interacting protein CIC1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.596691 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #45: protein, Pescadillo homolog

ProteinName: Pescadillo homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.984148 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #46: protein, Ribosome biogenesis protein 15

ProteinName: Ribosome biogenesis protein 15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.499186 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #47: protein, Ribosome biogenesis protein NOP53

ProteinName: Ribosome biogenesis protein NOP53 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.667832 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #48: protein, Ribosome biogenesis protein RLP7

ProteinName: Ribosome biogenesis protein RLP7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.621074 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #49: nucleic-acid, ITS2

nucleic acidName: ITS2Internal transcribed spacer / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: CCUUCUCAAA CAUUCUGUUU GGUAGUGAGU GAUACUCUUU GGAGUUAACU UGAAAUUGCU GGCCUUUUCA UUGGAUGUUU UUUUUCCAAA GAGAGGUUUC UCUGCGUGCU UGAGGUAUAA UGCAAGUACG GUCGUUUUAG GUUUUACCAA CUGCGGCUAA UCUUUUUUUA ...Sequence:
CCUUCUCAAA CAUUCUGUUU GGUAGUGAGU GAUACUCUUU GGAGUUAACU UGAAAUUGCU GGCCUUUUCA UUGGAUGUUU UUUUUCCAAA GAGAGGUUUC UCUGCGUGCU UGAGGUAUAA UGCAAGUACG GUCGUUUUAG GUUUUACCAA CUGCGGCUAA UCUUUUUUUA UACUGAGCGU AUUGGAACGU UAUCGAUAAG AAGAGAGCGU CUAGGCGAAC AAUGUUCUUA AA
MassTheoretical: 74.308391 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #50: protein, Nuclear GTP-binding protein NUG1

ProteinName: Nuclear GTP-binding protein NUG1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.798652 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #51: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 90 %

-
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: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionSampling size: 14 µm

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 30364
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 3JCT, 6N8J
Output model

+
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