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- EMDB-7445: Yeast nucleolar pre-60S ribosomal subunit (state 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-7445
TitleYeast nucleolar pre-60S ribosomal subunit (state 3)
Map data
SampleYeast nucleolar pre-60S ribosomal subunit:
(nucleic-acidNucleic acid) x 3 / (Ribosome biogenesis protein ...) x 6 / (60S ribosomal protein ...) x 22 / Protein MAK16 / Ribosome production factor 1 / Proteasome-interacting protein CIC1 / Nucleolar protein 16Nucleolus / rRNA-processing protein EBP2 / Pescadillo homolog / ATP-dependent RNA helicase HAS1 ...(nucleic-acidNucleic acid) x 3 / (Ribosome biogenesis protein ...) x 6 / (60S ribosomal protein ...) x 22 / Protein MAK16 / Ribosome production factor 1 / Proteasome-interacting protein CIC1 / Nucleolar protein 16Nucleolus / rRNA-processing protein EBP2 / Pescadillo homolog / ATP-dependent RNA helicase HAS1 / BRX1 associated peptide / Ribosomal RNA-processing protein 1 / ligand
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / snoRNA release from pre-rRNA / cell cycle DNA replication / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...L13a-mediated translational silencing of Ceruloplasmin expression / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / snoRNA release from pre-rRNA / cell cycle DNA replication / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / actomyosin contractile ring assembly / RNA-dependent ATPase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / 90S preribosome / preribosome, large subunit precursor / proteasome binding / negative regulation of mRNA splicing, via spliceosome / maturation of LSU-rRNA / ribosomal large subunit export from nucleus / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / ribosomal small subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome complex / cytoplasmic translation / helicase activity / protein binding, bridging / protein catabolic process / large ribosomal subunit rRNA binding / rRNA processing / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / nuclear envelope / ribosomal large subunit assembly / 5S rRNA binding / RNA helicase / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / RNA helicase activity / translation / cell cycle / mRNA binding / nucleolus / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Ribosomal protein L32e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L22/L17 superfamily / BRCT domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 ...Ribosomal protein L32e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L22/L17 superfamily / BRCT domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L14 / Ribosomal protein L7/L30 / Ribosomal protein L14, KOW motif / Ribosomal Protein L26/L24, KOW domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein L22p/L17e / RNA-binding domain superfamily / Ribosome biogenesis protein 15, RNA recognition motif / Helicase conserved C-terminal domain / Ribosomal protein L13, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosome biogenesis protein Nop16 / WD40 repeat, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 50S ribosomal protein L30e-like / Ribosomal protein L4 domain superfamily / Ribosomal protein L1-like / Ribosomal protein L15e core domain superfamily / Domain of unknown function DUF4217 / 60S ribosomal protein L4, C-terminal domain / Ribosome biogenesis protein BRX1 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / WD repeat BOP1/Erb1 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / DEAD/DEAH box helicase / Ribosomal protein L23 / Ribosomal protein L27e, conserved site / Trp-Asp (WD) repeats signature. / Domain of unknown function (DUF4217) / 60S ribosomal protein L4 C-terminal domain / BRCT domain, a BRCA1 C-terminus domain / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein 60S L18 and 50S L18e / DEAD-box subfamily ATP-dependent helicases signature. / Ribosomal protein L23 signature. / Ribosomal protein L22 signature. / Ribosomal protein L29 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30 signature. / Ribosomal protein L30e signature 1. / BOP1NT (NUC169) domain / Ribosomal protein L13 signature. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L27e signature. / Ribosomal protein L24 signature. / Ribosomal protein L34e signature. / Ribosome biogenesis protein Nop16 / Ribosomal L30 N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / WD domain, G-beta repeat / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / Ribosomal protein L1p/L10e family / Ribosomal L15 / Ribosomal L29 protein / Ribosomal protein L36e / Ribosomal protein L6e / Ribosomal protein L34e / Ribosomal protein L35Ae / Ribosomal protein L13e / Pescadillo N-terminus / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Ribosome production factor 1 / 60S ribosomal protein L4-A / Protein MAK16 / 60S ribosomal protein L30 / 60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosomal RNA-processing protein 1 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Proteasome-interacting protein CIC1 ...Ribosome production factor 1 / 60S ribosomal protein L4-A / Protein MAK16 / 60S ribosomal protein L30 / 60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosomal RNA-processing protein 1 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Proteasome-interacting protein CIC1 / 60S ribosomal protein L34-A / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / Ribosome biogenesis protein NSA1 / Pescadillo homolog / Ribosome biogenesis protein 15 / 60S ribosomal protein L18-A / 60S ribosomal protein L6-A / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Ribosome biogenesis protein BRX1 / 60S ribosomal protein L35-A / 60S ribosomal protein L25 / 60S ribosomal protein L20-A / Ribosomal 60S subunit protein L34A / 60S ribosomal protein L13 / Ribosomal 60S subunit protein L35A / Ribosomal 60S subunit protein L25 / Ribosomal 60S subunit protein L7A / 60S ribosomal protein L20 / RNA helicase / Ribosomal 60S subunit protein L32 / 60S ribosomal protein L6 / Ribosomal 60S subunit protein L4A / Ribosomal 60S subunit protein L18A / Ribosomal 60S subunit protein L38 / 60S ribosomal protein L27-A / rRNA-binding ribosome biosynthesis protein / Essential protein / Ribosomal 60S subunit protein L16A / Protein MAK16 / Ribosome biogenesis protein ERB1 / 60S ribosomal protein L7-A / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L33-A / 60S ribosomal protein L36-A / 60S ribosomal protein L15-A / 60S ribosomal protein L13-A
Biological speciesSaccharomyces cerevisiae BY4741 (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSanghai ZA / Miller L / Barandun J / Hunziker M / Chaker-Margot M / Klinge S
CitationJournal: Nature / Year: 2018
Title: Modular assembly of the nucleolar pre-60S ribosomal subunit.
Authors: Zahra Assur Sanghai / Linamarie Miller / Kelly R Molloy / Jonas Barandun / Mirjam Hunziker / Malik Chaker-Margot / Junjie Wang / Brian T Chait / Sebastian Klinge /
Abstract: Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly ...Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.
Validation ReportPDB-ID: 6cb1

SummaryFull reportAbout validation report
History
DepositionFeb 1, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseMar 14, 2018-
UpdateFeb 20, 2019-
Current statusFeb 20, 2019Processing 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
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cb1
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7445.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 480 pix.
= 624. Å
1.3 Å/pix.
x 480 pix.
= 624. Å
1.3 Å/pix.
x 480 pix.
= 624. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.035595495 - 0.10754153
Average (Standard dev.)0.00028619712 (±0.0031697818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 624.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z624.000624.000624.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0360.1080.000

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Supplemental data

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Sample components

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Entire Yeast nucleolar pre-60S ribosomal subunit

EntireName: Yeast nucleolar pre-60S ribosomal subunit / Number of components: 42

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Component #1: protein, Yeast nucleolar pre-60S ribosomal subunit

ProteinName: Yeast nucleolar pre-60S ribosomal subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast)

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Component #2: nucleic-acid, 35S pre-ribosomal RNA miscRNA

nucleic acidName: 35S pre-ribosomal RNA miscRNA / Class: RNA / Structure: OTHER / Synthetic: No
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 AGUAGCCAAA UGCCUCGUCA UCUAAUUAGU GACGCGCAUG AAUGGAUUAA CGAGAUUCCC ACUGUCCCUA UCUACUAUCU AGCGAAACCA CAGCCAAGGG AACGGGCUUG GCAGAAUCAG CGGGGAAAGA AGACCCUGUU GAGCUUGACU CUAGUUUGAC AUUGUGAAGA GACAUAGAGG GUGUAGAAUA AGUGGGAGCU UCGGCGCCAG UGAAAUACCA CUACCUUUAU AGUUUCUUUA CUUAUUCAAU GAAGCGGAGC UGGAAUUCAU UUUCCACGUU CUAGCAUUCA AGGUCCCAUU CGGGGCUGAU CCGGGUUGAA GACAUUGUCA GGUGGGGAGU UUGGCUGGGG CGGCACAUCU GUUAAACGAU AACGCAGAUG UCCUAAGGGG GGCUCAUGGA GAACAGAAAU CUCCAGUAGA ACAAAAGGGU AAAAGCCCCC UUGAUUUUGA UUUUCAGUGU GAAUACAAAC CAUGAAAGUG UGGCCUAUCG AUCCUUUAGU CCCUCGGAAU UUGAGGCUAG AGGUGCCAGA AAAGUUACCA CAGGGAUAAC UGGCUUGUGG CAGUACAAGC 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: 1.097477875 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: Saccharomyces cerevisiae BY4741 (yeast)

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Component #4: 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 UACUGAGCGU AUUGGAACGU UAUCGAUAAG AAGAGAGCGU CUAGGCGAAC AAUGUUCUUA AA
MassTheoretical: 74.308391 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast)

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Component #5: protein, Ribosome biogenesis protein NSA1

ProteinName: Ribosome biogenesis protein NSA1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.982457 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, Protein MAK16

ProteinName: Protein MAK16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.754605 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: 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 #9: 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 #10: 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 #11: protein, Ribosome production factor 1

ProteinName: Ribosome production factor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.184387 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: 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)

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Component #13: 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: protein, Nucleolar protein 16

ProteinName: Nucleolar protein 16Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.954447 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, Ribosome biogenesis protein BRX1

ProteinName: Ribosome biogenesis protein BRX1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.079852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: 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 #26: protein, Ribosome biogenesis protein YTM1

ProteinName: Ribosome biogenesis protein YTM1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.591789 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: 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 #28: 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 #29: 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 #30: 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 #31: 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 #32: 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 #33: 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 #34: protein, rRNA-processing protein EBP2

ProteinName: rRNA-processing protein EBP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.698714 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #35: 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 #36: 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 #37: protein, ATP-dependent RNA helicase HAS1

ProteinName: ATP-dependent RNA helicase HAS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.798348 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #38: protein, Ribosome biogenesis protein ERB1

ProteinName: Ribosome biogenesis protein ERB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.86068 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #39: protein, Ribosome biogenesis protein RLP7

ProteinName: Ribosome biogenesis protein RLP7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.210582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #40: protein, BRX1 associated peptide

ProteinName: BRX1 associated peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.400951 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #41: protein, Ribosomal RNA-processing protein 1

ProteinName: Ribosomal RNA-processing protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.250531 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #42: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.56 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 31419
3D reconstructionSoftware: RELION / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Output model

+
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