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- EMDB-10838: Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-10838
TitleRix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)
Map data
SampleRix1-Rea1 pre-60S assembly particle - 60S core portion
  • (nucleic-acidNucleic acid) x 3
  • Probable metalloprotease ARX1
  • rRNA-processing protein CGR1
  • (60S ribosomal protein ...) x 37
  • Bud site selection protein 20
  • Pre-rRNA-processing protein IPI1
  • (Ribosome assembly ...) x 2
  • (Nucleolar GTP-binding protein ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • Nuclear GTP-binding protein NUG1
  • Protein SDA1
  • Eukaryotic translation initiation factor 6
  • UPF0642 protein YBL028C
  • (ligand) x 3
Function / homology
Function and homology information


regulation of ribosomal subunit export from nucleus / protein-RNA complex remodeling / 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 / traversing start control point of mitotic cell cycle / Hydrolases / positive regulation of ATPase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit binding ...regulation of ribosomal subunit export from nucleus / protein-RNA complex remodeling / 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 / traversing start control point of mitotic cell cycle / Hydrolases / positive regulation of ATPase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit binding / pre-mRNA 5'-splice site binding / ribosomal subunit export from nucleus / ATPase activator activity / preribosome, large subunit precursor / ribonucleoprotein complex assembly / negative regulation of mRNA splicing, via spliceosome / regulation of translational fidelity / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / mature ribosome assembly / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / metallopeptidase activity / rRNA processing / large ribosomal subunit rRNA binding / macroautophagy / cytoplasmic translation / actin cytoskeleton organization / ribosome biogenesis / large ribosomal subunit / 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 / cell cycle / GTPase activity / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L37e, conserved site / Ribosomal protein L2, domain 2 / Nucleolar GTP-binding protein 2, N-terminal domain / NLE / NOG, C-terminal / Uncharacterised domain NUC130/133, N-terminal / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Zinc finger C2H2-type ...Ribosomal protein L37e, conserved site / Ribosomal protein L2, domain 2 / Nucleolar GTP-binding protein 2, N-terminal domain / NLE / NOG, C-terminal / Uncharacterised domain NUC130/133, N-terminal / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Zinc finger C2H2-type / Ribosomal protein L2, domain 3 / Nucleotide-binding alpha-beta plait domain superfamily / Guanine nucleotide-binding protein-like 3, N-terminal domain / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L19/L19e, domain 1 / Armadillo-type fold / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / WD40-repeat-containing domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L23/L15e core domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L13e, conserved site / KOW / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L5 eukaryotic/L18 archaeal / Cgr1-like / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L13 / Ribosomal protein L24/L26, conserved site / Zinc-binding ribosomal protein / Ribosomal protein L7, eukaryotic / GTP binding domain / SDA1 domain / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Nucleolar GTP-binding protein 1, Rossman-fold domain / TRASH domain / Ribosomal protein L37ae/L37e / Ribosomal protein L29, conserved site / Ribosomal protein L21e, conserved site / Matrin/U1-C-like, C2H2-type zinc finger / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L2, conserved site / Zinc finger, double-stranded RNA binding / Ribosome biogenesis protein Alb1 / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Pre-rRNA-processing protein Ipi1, N-terminal / Ribosomal protein L15e core domain superfamily / Nucleolar GTP-binding protein 1 / Nucleolar GTP-binding protein 2 / Ribosomal protein L2, C-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Sda1 / Ribosomal protein L7Ae/L8/Nhp2 family / Uncharacterised protein family UPF0642 / WD40 repeat, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L31e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / Ribosomal protein L7Ae conserved site / Ribosomal protein L14e domain / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L32e superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily
60S ribosomal protein L4-A / Ribosome assembly factor MRT4 / UPF0642 protein YBL028C / 60S ribosomal protein L32 / 60S ribosomal protein L14-A / 60S ribosomal protein L3 / 60S ribosomal protein L16-A / 60S ribosomal protein L5 / Ribosome assembly protein 4 / 60S ribosomal protein L8-A ...60S ribosomal protein L4-A / Ribosome assembly factor MRT4 / UPF0642 protein YBL028C / 60S ribosomal protein L32 / 60S ribosomal protein L14-A / 60S ribosomal protein L3 / 60S ribosomal protein L16-A / 60S ribosomal protein L5 / Ribosome assembly protein 4 / 60S ribosomal protein L8-A / 60S ribosomal protein L37-A / Nuclear GTP-binding protein NUG1 / 60S ribosomal protein L6-A / 60S ribosomal protein L38 / rRNA-processing protein CGR1 / Protein SDA1 / Nucleolar GTP-binding protein 2 / 60S ribosomal protein L34-A / 60S ribosomal protein L21-A / Nucleolar GTP-binding protein 1 / Probable metalloprotease ARX1 / Ribosome biogenesis protein RLP24 / Bud site selection protein 20 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L30 / Ribosome biogenesis protein NSA2 / 60S ribosomal protein L35-A / 60S ribosomal protein L36-A / Ribosome biogenesis protein ALB1 / Pre-rRNA-processing protein IPI1 / 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 L33-A / 60S ribosomal protein L15-A / 60S ribosomal protein L19-A / 60S ribosomal protein L22-A / 60S ribosomal protein L11-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 L1-A / 60S ribosomal protein L2-A / 60S ribosomal protein L18-A / 60S ribosomal protein L12-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 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: 6ylg

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: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ylg
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ylg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10838.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.)
1.06 Å/pix.
x 400 pix.
= 423.6 Å
1.06 Å/pix.
x 400 pix.
= 423.6 Å
1.06 Å/pix.
x 400 pix.
= 423.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.049282763 - 0.13033897
Average (Standard dev.)0.00013768185 (±0.006713846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z423.600423.600423.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0490.1300.000

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Supplemental data

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Half map: #2

Fileemd_10838_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_10838_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Rix1-Rea1 pre-60S assembly particle - 60S core portion

EntireName: Rix1-Rea1 pre-60S assembly particle - 60S core portion
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Number of components: 59

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Component #1: protein, Rix1-Rea1 pre-60S assembly particle - 60S core portion

ProteinName: Rix1-Rea1 pre-60S assembly particle - 60S core portion
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: 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)

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Component #3: 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)

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Component #4: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Probable metalloprotease ARX1

ProteinName: Probable metalloprotease ARX1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.290336 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, rRNA-processing protein CGR1

ProteinName: rRNA-processing protein CGR1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.460057 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: 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 #8: 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 #9: 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 #10: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.764828 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: 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 #12: 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 #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 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 #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 L11-A

ProteinName: 60S ribosomal protein L11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.755691 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, Pre-rRNA-processing protein IPI1

ProteinName: Pre-rRNA-processing protein IPI1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.928895 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: 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 #24: 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 #25: 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 #26: 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 #27: 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 #28: 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 #29: 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)

+
Component #30: 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)

+
Component #31: 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)

+
Component #32: 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)

+
Component #33: 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)

+
Component #34: 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)

+
Component #35: protein, Ribosome biogenesis protein ALB1

ProteinName: Ribosome biogenesis protein ALB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.322037 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #36: 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)

+
Component #37: 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)

+
Component #38: 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)

+
Component #39: 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)

+
Component #40: 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)

+
Component #41: 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)

+
Component #42: 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)

+
Component #43: 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)

+
Component #44: 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)

+
Component #45: protein, Nucleolar GTP-binding protein 2

ProteinName: Nucleolar GTP-binding protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.58559 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #46: 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)

+
Component #47: protein, 60S ribosomal protein L1-A

ProteinName: 60S ribosomal protein L1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.524799 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #48: 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)

+
Component #49: protein, 60S ribosomal protein L12-A

ProteinName: 60S ribosomal protein L12-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.850621 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #50: 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)

+
Component #51: 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 #52: protein, Protein SDA1

ProteinName: Protein SDA1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.755578 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #53: 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)

+
Component #54: protein, Ribosome assembly protein 4

ProteinName: Ribosome assembly protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.106781 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #55: 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)

+
Component #56: 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)

+
Component #57: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #58: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #59: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 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: 75 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image acquisition

Image acquisitionSampling size: 5 µm

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 114398
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3 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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