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- EMDB-4560: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles -

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Basic information

Entry
Database: EMDB / ID: EMD-4560
TitleCryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Map data
SampleLsg1-TAP 60s ribosomal subunit
  • (nucleic-acidNucleic acid) x 3
  • (60S ribosomal protein ...) x 38
  • Eukaryotic translation initiation factor 6
  • Cytoplasmic 60S subunit biogenesis factor REH1
  • 60S ribosomal export protein NMD3
  • Large subunit GTPase 1
  • uL1
  • Ubiquitin-60S ribosomal protein L40
  • ligand
Function / homology
Function and homology information


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 / SRP-dependent cotranslational protein targeting to membrane / L13a-mediated translational silencing of Ceruloplasmin expression / conjugation with cellular fusion / ascospore formation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus ...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 / SRP-dependent cotranslational protein targeting to membrane / L13a-mediated translational silencing of Ceruloplasmin expression / conjugation with cellular fusion / ascospore formation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / mating projection tip / pre-mRNA 5'-splice site binding / Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides / 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 / preribosome, large subunit precursor / response to cycloheximide / regulation of translational fidelity / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / ribosomal large subunit biogenesis / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mature ribosome assembly / cytoplasmic translation / translational termination / assembly of large subunit precursor of preribosome / translation initiation factor activity / maintenance of translational fidelity / modification-dependent protein catabolic process / large ribosomal subunit rRNA binding / rRNA processing / protein tag / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / protein ubiquitination / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ubiquitin protein ligase binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 superfamily / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal ...Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 superfamily / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Zinc finger C2H2 type domain signature. / Ribosomal protein L32e superfamily / Ribosomal protein L6, alpha-beta domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L35A superfamily / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ubiquitin / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L24e, conserved site / 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 L15e core domain superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L35Ae, conserved site / Ribosomal L29e protein family / Ribosomal protein L6e / Ribosomal protein L31e / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L27e protein family / Ribosomal L37ae protein family / Ribosomal protein L21e / Ribosomal L38e protein family / Ribosomal protein L37e / eIF-6 family / 50S ribosome-binding GTPase / Ribosomal protein L14 / Ribosomal protein L23, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / NMD3 family / Ribosomal L30 N-terminal domain / C2H2 type zinc-finger (2 copies) / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L36e / Ribosomal L40e family / 60S ribosomal protein L19 / Ubiquitin family / Ribosomal protein L14 / Ribosomal protein L7/L30 / Ribosomal export protein Nmd3 / Zinc finger protein 622/Rei1/Reh1 / ZN622/Rei1/Reh1, zinc finger C2H2-type / Ribosomal protein L14, KOW motif
60S ribosomal protein L18-A / 60S ribosomal protein L8-A / 60S ribosomal protein L16-B / 60S ribosomal protein L5 / 60S ribosomal protein L35-A / 60S ribosomal protein L3 / 60S ribosomal protein L30 / 60S ribosomal protein L4-A / 60S ribosomal protein L32 / 60S ribosomal protein L14-A ...60S ribosomal protein L18-A / 60S ribosomal protein L8-A / 60S ribosomal protein L16-B / 60S ribosomal protein L5 / 60S ribosomal protein L35-A / 60S ribosomal protein L3 / 60S ribosomal protein L30 / 60S ribosomal protein L4-A / 60S ribosomal protein L32 / 60S ribosomal protein L14-A / Large subunit GTPase 1 / 60S ribosomal export protein NMD3 / 60S ribosomal protein L10 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Cytoplasmic 60S subunit biogenesis factor REH1 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L19-A / 60S ribosomal protein L28 / 60S ribosomal protein L2-A / 60S ribosomal protein L36-A / 60S ribosomal protein L24-A / 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 L29 / 60S ribosomal protein L23-A / 60S ribosomal protein L15-A / 60S ribosomal protein L22-A / 60S ribosomal protein L11-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 60S ribosomal protein L42-A / 60S ribosomal protein L13-A
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKargas V / Warren AJ
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Bloodwise12048 United Kingdom
Medical Research Council (United Kingdom)105161083 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren /
Abstract: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.
Validation ReportPDB-ID: 6qik

SummaryFull report
PDB-ID: 6qt0

SummaryFull report
About validation report
History
DepositionJan 20, 2019-
Header (metadata) releaseJun 26, 2019-
Map releaseJun 26, 2019-
UpdateJul 10, 2019-
Current statusJul 10, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qik
  • Surface level: 0.07
  • 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_4560.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 383.4 Å
1.07 Å/pix.
x 360 pix.
= 383.4 Å
1.07 Å/pix.
x 360 pix.
= 383.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.28670764 - 0.5598857
Average (Standard dev.)0.0026033714 (±0.02189199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z383.400383.400383.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2870.5600.003

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Supplemental data

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Sample components

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Entire Lsg1-TAP 60s ribosomal subunit

EntireName: Lsg1-TAP 60s ribosomal subunit / Number of components: 49

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Component #1: protein, Lsg1-TAP 60s ribosomal subunit

ProteinName: Lsg1-TAP 60s ribosomal subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: nucleic-acid, 25S ribosomal RNA

nucleic acidName: 25S ribosomal RNA / 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 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: Saccharomyces cerevisiae (baker's yeast)

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Component #3: 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 #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, 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 #6: 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 #7: 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 #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 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 #10: protein, 60S ribosomal protein L16-B

ProteinName: 60S ribosomal protein L16-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.296236 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: 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 #12: 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 #13: 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 #14: 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 #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 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 #17: 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 #18: 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 #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 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 #21: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.319527 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: 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 #23: 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 #24: 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 #25: 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 #26: 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 #27: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.691884 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: 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 #29: 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 #30: 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 #31: 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 #32: 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 #33: 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 #34: 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 #35: 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 #36: 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 #37: 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 #38: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.246658 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #39: 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 #40: 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 #41: protein, Cytoplasmic 60S subunit biogenesis factor REH1

ProteinName: Cytoplasmic 60S subunit biogenesis factor REH1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.763773 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #42: protein, 60S ribosomal export protein NMD3

ProteinName: 60S ribosomal export protein NMD3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.167047 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #43: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.661717 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #44: protein, Large subunit GTPase 1

ProteinName: Large subunit GTPase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.838445 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #45: protein, uL1

ProteinName: uL1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.889996 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #46: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.583077 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #47: nucleic-acid, 5S ribosomal RNA

nucleic acidName: 5S 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: Saccharomyces cerevisiae (baker's yeast)

+
Component #48: nucleic-acid, 5.8S ribosomal RNA

nucleic acidName: 5.8S 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 (baker's yeast)

+
Component #49: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 63 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 260853
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 4V88
Output model

+
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