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- EMDB-11608: Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation c... -

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Basic information

Entry
Database: EMDB / ID: EMD-11608
TitleStructure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex
Map data
SampleABCE1-bound 43S PIC
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 31
  • Ubiquitin-40S ribosomal protein S31
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Eukaryotic translation initiation factor 3 subunit J
  • Translation initiation factor RLI1
  • (ligand) x 4
Function / homology
Function and homology information


ribosome disassembly / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation ...ribosome disassembly / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity / rRNA export from nucleus / ribosomal subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / preribosome, small subunit precursor / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / rescue of stalled ribosome / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / ribosomal small subunit binding / maturation of SSU-rRNA / regulation of translational fidelity / ribosomal large subunit biogenesis / small-subunit processome / ribosomal small subunit biogenesis / protein kinase A catalytic subunit binding / positive regulation of protein kinase activity / cellular response to amino acid starvation / translation initiation factor activity / translational initiation / ribosome assembly / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / protein kinase C binding / positive regulation of translation / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / protein tag / rRNA processing / cytoplasmic stress granule / cytoplasmic translation / ribosome binding / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / protein localization / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / protein ubiquitination / translation / negative regulation of gene expression / iron ion binding / ATPase / positive regulation of protein phosphorylation / mRNA binding / G protein-coupled receptor signaling pathway / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / K Homology domain, type 2 / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Plectin/S10, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal ...Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / K Homology domain, type 2 / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Plectin/S10, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / AAA+ ATPase domain / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / KOW / Ribosomal protein S12/S23 / Ribosomal protein S30 / RNase L inhibitor RLI-like, possible metal-binding domain / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / ABC transporter-like / Zinc-binding ribosomal protein / WD40 repeat / Ribosomal protein S26e / Ribosomal protein S8e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S3, C-terminal / Ribosomal protein S6e / Ribosomal protein S3Ae / Ribosomal protein S10 / RNA-binding S4 domain / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / Ribosomal protein S27a / Ribosomal protein S13-like, H2TH / Nucleic acid-binding, OB-fold / Ribosomal protein S5 / Ribosomal protein S8e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein L23/L15e core domain superfamily / RLI1 / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Eukaryotic translation initiation factor 3 subunit J / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S2, conserved site / K homology domain-like, alpha/beta / ABC transporter, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S4/S9 / Winged helix DNA-binding domain superfamily / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S8 / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / RLI, domain 1 / Ribosomal protein S8 superfamily
40S ribosomal protein S5 / 40S ribosomal protein S0-A / 40S ribosomal protein S1-A / 40S ribosomal protein S27-A / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S20 / 40S ribosomal protein S14-B / 40S ribosomal protein S29-A / 40S ribosomal protein S26-B / 40S ribosomal protein S12 ...40S ribosomal protein S5 / 40S ribosomal protein S0-A / 40S ribosomal protein S1-A / 40S ribosomal protein S27-A / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S20 / 40S ribosomal protein S14-B / 40S ribosomal protein S29-A / 40S ribosomal protein S26-B / 40S ribosomal protein S12 / 40S ribosomal protein S15 / Translation initiation factor RLI1 / Eukaryotic translation initiation factor 3 subunit J / 40S ribosomal protein S10-A / 40S ribosomal protein S25-A / 40S ribosomal protein S7-A / 40S ribosomal protein S3 / 40S ribosomal protein S2 / 40S ribosomal protein S23-A / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S19-A / 40S ribosomal protein S21-A / 40S ribosomal protein S22-A / 40S ribosomal protein S24-A / 40S ribosomal protein S17-B / 40S ribosomal protein S30-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S18-A / 40S ribosomal protein S28-A
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMackens-Kiani T / Kratzat H / Cheng J / Berninghausen O / Becker T / Beckmann R
Funding support Germany, France, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: EMBO J / Year: 2021
Title: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes.
Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine ...Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine / Thomas Becker / Roland Beckmann /
Abstract: In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. ...In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionAug 13, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBe / 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 height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a1g
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a1g
  • 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_11608.map.gz / Format: CCP4 / Size: 347.6 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 450 pix.
= 476.55 Å
1.06 Å/pix.
x 450 pix.
= 476.55 Å
1.06 Å/pix.
x 450 pix.
= 476.55 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: 0.04 / Movie #1: 0.018
Minimum - Maximum-0.03182269 - 0.13003638
Average (Standard dev.)-0.000109540495 (±0.004068555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 476.55002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z476.550476.550476.550
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0320.130-0.000

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Supplemental data

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Additional map: post-processed map

Fileemd_11608_additional_1.map
Annotationpost-processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: local resolution filtered map

Fileemd_11608_additional_2.map
Annotationlocal resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: #1

Fileemd_11608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_11608_half_map_2.map
Projections & Slices
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Sample components

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Entire ABCE1-bound 43S PIC

EntireName: ABCE1-bound 43S PIC / Number of components: 41

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Component #1: protein, ABCE1-bound 43S PIC

ProteinName: ABCE1-bound 43S PIC / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #2: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ...Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCGG AUUUCCAACG GGGCCUUUCC UUCUGGCUAA CCUUGAGCUU GGCGAACCAG GACUUUUACU UUGAAAAAAU UAGAGUGUUC AAAGCAGGCG UAUUGCUCGA AUAUAUUAGC AUGGAAUAAU AGAAUAGGAC GUUUGGUUCU AUUUUGUUGG UUUCUAGGAC CAUCGUAAUG AUUAAUAGGG ACGGUCGGGG GCAUCAGUAU UCAAUUGUCA GAGGUGAAAU UCUUGGAUUU AUUGAAGACU AACUACUGCG AAAGCAUUUG CCAAGGACGU UUUCAUUAAU CAAGAACGAA AGUUAGGGGA UCGAAGAUGA UCAGAUACCG UCGUAGUCUU AACCAUAAAC UAUGCCGACU AGGGAUCGGG UGGUGUUUUU UUAAUGACCC ACUCGGCACC UUACGAGAAA UCAAAGUCUU UGGGUUCUGG GGGGAGUAUG GUCGCAAGGC UGAAACUUAA AGGAAUUGAC GGAAGGGCAC CACCAGGAGU GGAGCCUGCG GCUUAAUUUG ACUCAACACG GGGAAACUCA CCAGGUCCAG ACACAAUAAG GAUUGACAGA UUGAGAGCUC UUUCUUGAUU UUGUGGGUGG UGGUGCAUGG CCGUUCUUAG UUGGUGGAGU GAUUUGUCUG CUUAAUUGCG AUAACGAACG AGACCUUAAC CUACUAAAUA GUGGUGCUAG CAUUUGCUGG UUAUCCACUU CUUAGAGGGA CUAUCGGUUU CAAGCCGAUG GAAGUUUGAG GCAAUAACAG GUCUGUGAUG CCCUUAGACG UUCUGGGCCG CACGCGCGCU ACACUGACGG AGCCAGCGAG UCUAACCUUG GCCGAGAGGU CUUGGUAAUC UUGUGAAACU CCGUCGUGCU GGGGAUAGAG CAUUGUAAUU AUUGCUCUUC AACGAGGAAU UCCUAGUAAG CGCAAGUCAU CAGCUUGCGU UGAUUACGUC CCUGCCCUUU GUACACACCG CCCGUCGCUA GUACCGAUUG AAUGGCUUAG UGAGGCCUCA GGAUCUGCUU AGAGAAGGGG GCAACUCCAU CUCAGAGCGG AGAAUUUGGA CAAACUUGGU CAUUUAGAGG AACUAAAAGU CGUAACAAGG UUUCCGUAGG UGAACCUGCG GAAGGAUCAU U
MassTheoretical: 570.58525 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #3: protein, 40S ribosomal protein S0-A

ProteinName: 40S ribosomal protein S0-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.811074 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.314684 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.08485 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.167926 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.181445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.000492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.081549 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.272149 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.928748 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, 40S ribosomal protein S14-B

ProteinName: 40S ribosomal protein S14-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.446426 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, 40S ribosomal protein S21-A

ProteinName: 40S ribosomal protein S21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.758829 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.518867 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.942699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.23165 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, 40S ribosomal protein S26-B

ProteinName: 40S ribosomal protein S26-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.022989 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.762195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, 40S ribosomal protein S30-A

ProteinName: 40S ribosomal protein S30-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.779086 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.265591 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.631713 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.908338 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, 40S ribosomal protein S10-A

ProteinName: 40S ribosomal protein S10-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.042562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028008 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.659216 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, 40S ribosomal protein S17-B

ProteinName: 40S ribosomal protein S17-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.268545 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.940443 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, 40S ribosomal protein S19-A

ProteinName: 40S ribosomal protein S19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.81093 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.363321 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, 40S ribosomal protein S25-A

ProteinName: 40S ribosomal protein S25-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.540301 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, 40S ribosomal protein S29-A

ProteinName: 40S ribosomal protein S29-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.335303 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, Ubiquitin-40S ribosomal protein S31

ProteinName: Ubiquitin-40S ribosomal protein S31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.388049 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, Guanine nucleotide-binding protein subunit beta-like protein

ProteinName: Guanine nucleotide-binding protein subunit beta-like protein
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.151484 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #35: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.116281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #36: protein, Eukaryotic translation initiation factor 3 subunit J

ProteinName: Eukaryotic translation initiation factor 3 subunit J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.611225 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #37: protein, Translation initiation factor RLI1

ProteinName: Translation initiation factor RLI1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.714469 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 80 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #39: ligand, ZINC ION

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

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Component #40: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #41: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 25245
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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