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- EMDB-0192: Structure of the rabbit 80S ribosome stalled on globin mRNA at th... -

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Basic information

Entry
Database: EMDB / ID: 0192
TitleStructure of the rabbit 80S ribosome stalled on globin mRNA at the stop codon
Map dataRabbit 80S stalled on globin mRNA at the stop codon
SampleRabbit 80S ribosome stalled on globin mRNA at the stop codon
  • Ribosome
  • (RACK1Receptor for activated C kinase 1) x 2
  • (nucleic-acidNucleic acid) x 6
  • uS2
  • (40S ribosomal protein ...) x 6
  • uS5
  • uS3
  • eS4
  • (Ribosomal protein ...) x 15
  • eS8
  • eS10
  • uS15
  • uS11
  • uS19
  • eS17
  • uS13
  • eS19
  • uS10
  • eS21
  • uS12
  • eS24
  • eS25
  • eS26
  • uS14
  • eRF1(AAQ)
  • ATP binding cassette subfamily E member 1
  • uL3
  • uL4
  • (60S ribosomal protein ...) x 5
  • uL30
  • uL6
  • eL13
  • uL13
  • uL22
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • uL23
  • uL15
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • uL29
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL28
  • uL10
  • eL8
  • nascent chain
  • uL1
  • (ligand) x 4
Function / homologyRibosomal protein S17, archaeal/eukaryotic / Ribosomal protein L22/L17 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix-like DNA-binding domain superfamily ...Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L22/L17 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / RLI, domain 1 / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L14 superfamily / Ribosomal protein L10e/L16 superfamily / Ubiquitin-like domain superfamily / Ribosomal protein L14 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S4/S9 N-terminal domain / 4Fe-4S binding domain / ABC transporter / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7/L30 / Ubiquitin-like protein FUBI / Ribosomal protein L21 superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / S27a-like superfamily / Ribosomal protein L36e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein L5, C-terminal / 50S ribosomal protein L30e-like / Ribosomal protein L22p/L17e / Ribosomal protein S7, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal L28e/Mak16 / Ribosomal protein S7 domain / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein L1-like / Ribosomal protein L30e, conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein S19 / Ribosomal protein L14p/L23e / Ubiquitin conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein S7 signature. / Ribosomal protein L39e signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal_S17 N-terminal / Ribosomal L18 C-terminal region / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S17 signature. / KH domain
Function and homology information
SourceOryctolagus cuniculus (rabbit) / Homo sapiens (human) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsJuszkiewicz S / Chandrasekaran V / Lin Z / Kraatz S / Ramakrishnan V / Hegde RS
CitationJournal: Mol. Cell / Year: 2018
Title: ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
Authors: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde
Abstract: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.
Validation ReportPDB-ID: 6hcf

SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Oct 17, 2018 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hcf
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0192.map.gz (map file in CCP4 format, 180473 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
356 pix
1.52 Å/pix.
= 541.12 Å
356 pix
1.52 Å/pix.
= 541.12 Å
356 pix
1.52 Å/pix.
= 541.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.52 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.46443152 - 0.8349833
Average (Standard dev.)0.0014852848 (0.027612282)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions356356356
Origin0.00.00.0
Limit355.0355.0355.0
Spacing356356356
CellA=B=C: 541.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.521.521.52
M x/y/z356356356
origin x/y/z0.0000.0000.000
length x/y/z541.120541.120541.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS356356356
D min/max/mean-0.4640.8350.001

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Supplemental data

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Mask #1

Fileemd_0192_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Rabbit 80S ribosome stalled on globin mRNA at the stop codon

EntireName: Rabbit 80S ribosome stalled on globin mRNA at the stop codon
Number of components: 94

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Component #1: protein, Rabbit 80S ribosome stalled on globin mRNA at the stop codon

ProteinName: Rabbit 80S ribosome stalled on globin mRNA at the stop codon
Recombinant expression: No
MassTheoretical: 4.3 MDa

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Component #2: protein, Ribosome

ProteinName: Ribosome / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #3: protein, RACK1

ProteinName: RACK1Receptor for activated C kinase 1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCGCCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACUGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCCUGGCGG AGCGCUGAGA AGACGGUCGA ACUUGACUAU CUAGAGGAAG UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUA
MassTheoretical: 602.778875 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #5: protein, uS2

ProteinName: uS2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.958016 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #6: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: protein, uS5

ProteinName: uS5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.327395 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #8: protein, uS3

ProteinName: uS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.715344 kDa
SourceSpecies: Rabbit (rabbit)

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Component #9: protein, eS4

ProteinName: eS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.654869 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #10: protein, Ribosomal protein S5

ProteinName: Ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Rabbit (rabbit)

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Component #11: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Rabbit (rabbit)

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Component #12: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Rabbit (rabbit)

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Component #13: protein, eS8

ProteinName: eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #14: protein, Ribosomal protein S9 (Predicted)

ProteinName: Ribosomal protein S9 (Predicted)Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Rabbit (rabbit)

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Component #15: protein, eS10

ProteinName: eS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Rabbit (rabbit)

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Component #16: protein, Ribosomal protein S11

ProteinName: Ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Rabbit (rabbit)

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Component #17: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Rabbit (rabbit)

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Component #18: protein, uS15

ProteinName: uS15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Rabbit (rabbit)

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Component #19: protein, uS11

ProteinName: uS11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.133984 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #20: protein, uS19

ProteinName: uS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.049182 kDa
SourceSpecies: Rabbit (rabbit)

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Component #21: protein, Ribosomal protein S16

ProteinName: Ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Rabbit (rabbit)

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Component #22: protein, eS17

ProteinName: eS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.552119 kDa
SourceSpecies: Rabbit (rabbit)

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Component #23: protein, uS13

ProteinName: uS13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Rabbit (rabbit)

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Component #24: protein, eS19

ProteinName: eS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.10664 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #25: protein, uS10

ProteinName: uS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Rabbit (rabbit)

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Component #26: protein, eS21

ProteinName: eS21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #27: protein, Ribosomal protein S15a

ProteinName: Ribosomal protein S15aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Rabbit (rabbit)

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Component #28: protein, uS12

ProteinName: uS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #29: protein, eS24

ProteinName: eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.107924 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #30: protein, eS25

ProteinName: eS25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Rabbit (rabbit)

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Component #31: protein, eS26

ProteinName: eS26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.047532 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #32: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Rabbit (rabbit)

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Component #33: protein, Ribosomal protein S28

ProteinName: Ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Rabbit (rabbit)

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Component #34: protein, uS14

ProteinName: uS14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.690821 kDa
SourceSpecies: Rabbit (rabbit)

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Component #35: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.498884 kDa
SourceSpecies: Rabbit (rabbit)

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Component #36: protein, Ribosomal protein S27a

ProteinName: Ribosomal protein S27aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Rabbit (rabbit)

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Component #37: protein, RACK1

ProteinName: RACK1Receptor for activated C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Rabbit (rabbit)

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Component #38: protein, eRF1(AAQ)

ProteinName: eRF1(AAQ) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.264926 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #39: protein, ATP binding cassette subfamily E member 1

ProteinName: ATP binding cassette subfamily E member 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.405234 kDa
SourceSpecies: Rabbit (rabbit)

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Component #40: nucleic-acid, 28S ribosomal RNA

Nucleic-acidName: 28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAA AAGAAACUAA CCAGGAUUCC CUCAGUAACG GCGAGUGAAC AGGGAAGAGC CCAGCGCCGA AUCCCCGCCC CGCGGCGGGG CGCGGGAAAU GUGGCGUACG GAAGACCCAC UCCCCGGCGC CGGGGGGCCC AAGUCCUUCU GAUCGAGGCC CAGCCCGUGG ACGGUGUGAG GCCGGUAGCG GCCCCCGGCG CGCCGGGCCC GGGUCUUCCC GGAGUCGGGU UGCUUGGGAA UGCAGCCCAA AGCGGGUGGU AAACUCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAAGGGA AAGUUGAAAA GAACUUUGAA GAGAGAGUUC AAGAGGGCGU GAAACCGUUA AGAGGUAAAC GGGUGGGGUC CGCGCAGUCC GCCCGGAGGA UUCAACCCGG CGGCGCGGUC CGGCCGUGCC GGCGGGGCGG AUCUCCCGCU CCCGUCGGCG GGGGACCGCC CCCCGGCCGG CGACCGGCCG CCGCCGGGCG CAUUUCCACC GCGGCGGUGC GCCGCGACCG GCUCCGGGAC GGCUGGGAAG GCCCCGGCGG GGAAGGUGGC CCGGGGGCCC CGGGUGUUAC AGCCCCGCCC CGGCAGCAGC AGCUCGCCGA AUCCCGGGGC CGAGGGAGCG AGACCCGUGC GCCGCGCUCU CCCCCCUCGG GGGGGCCGGG CCACCCCUCC CACGGCGCGA CCGCUCUCCC ACCCGGGGGG CGGGGCGGAC UGUCCCCAGU GCGCCCCGGG CGGGUCGCGC CGUCGGGCCC GGGGGAGGUU CUCUCGGGGC CACGCGUCCC CCGCGAGCGC ACGGGGUCGG CGGCGAUGUC GGCUACCCAC CCGACCCGUC UUGAAACACG GACCAAGGAG UCUAACACGU GCGCGAGUCG GGGGCUACGA AAGCCGCCGU GGCGCAAUGA AGGUGAAGGC CGGCGGCGCG CCGCCGGCCG AGGUGGGAUC CCGAGGCCUU CCAGUCCGCC GAGGGCGCAC CACCGGCCCG UCUCGCCCGC CGCGCCGGGG AGGUGGAGCA CGAGCGCACG UGUUAGGACC CGAAAGAUGG UGAACUAUGC CUGGGCAGGG CGAAGCCAGA GGAAACUCUG GUGGAGGUCC GUAGCGGUCC UGACGUGCGA AUCGGUCGUC CGACCUGGGU AUAGGGGCGA AAGACUAAUC GAACCAUCUA GUAGCUGGUU CCCUCCAAAG UUUCCCUCAG GAUAGCUGGC GCUCUCCGCA GUUUUAUCCG GUAAAGCGAA UGAUUAGAGG UCUUGGGGCC GAAACGAUCU CAACCUAUUC UCAAACUUUA AAUGGGUAAG AAGCCCGGCU CGCUGGUGUG GAGCCGGGCG UGGAAUGCGA GUGCCUAGUG GGCCACUUUU GGUAAGCAGA ACUGGCGCUG CGGGAUGAAC CGAACGCCGG GUUAAGGCGC CCGAUGCCGA CGCUCAUCAG ACCCCAGAAA AGGUGUUGGU UGAUAUAGAC AGCAGGAUGG UGGCCAUGGA AGUCGGAAUC CGCUAAGGAG UGUGUAACAA CUCACCUGCC GAAUCAACUA GCCCUGAAAA UGGAUGGCGC UGGAGCGUCG GGCCCAUACC CGGCCGUCGC UGGCAGUCGG CAGAGCGAGA AAGAGAGUGG CGCGGACGCU ACGCCGCGAC GAGUAGGAGG GCCGCUGCGG UGAGCCUUGA AGCCUAGGGC GCGGGCCCGG GUGGAGCCGC CGCAGGUGCA GAUCUUGGUG GUAGUAGCAA AUAUUCAAAC GAGAACUUUG AAGGCCGAAG UGGAGAAGGG UUCCAUGUGA ACAGCAGUUG AACAUGGGUC AGUCGGUCCU GAGAGAUGGG CGAGCGCCGU UCCGAAGGGA CGGGCGAUGG CCUCCGUUGC CCUCAGCCGA UCGAAAGGGA GUCGGGUUCA GAUCCCCGAA UCCGGAGUGG CGGAGAUGGG CGCCGCGAGG CGUCCAGUGC GGUAACGCGA CCGAUCCCGG AGAAGCCGGC GGGAGCCCCG GGGAGAGUUC UCUUUUCUUU GUGAAGGGCA GGGCGCCCUG GAAUGGGUUC GCCCCGAGAG AGGGGCCCGU GCCUUGGAAA GCGUCGCGGU UCCGGCGGCG UCCGGUGAGC UCUCGCUGGC CCUUGAAAAU CCGGGGGAGA GGGUGUAAAU CUCGCGCCGG GCCGUACCCA UAUCCGCAGC AGGUCUCCAA GGUGAACAGC CUCUGGCAUG UUGGAACAAU GUAGGUAAGG GAAGUCGGCA AGCCGGAUCC GUAACUUCGG GAUAAGGAUU GGCUCUAAGG GCUGGCAGCC GACUUAGAAC UGGUGCGGAC CAGGGGAAUC CGACUGUUUA AUUAAAACAA AGCAUCGCGA AGGCCCGCGG CGGGUGUUGA CGCGAUGUGA UUUCUGCCCA GUGCUCUGAA UGUCAAAGUG AAGAAAUUCA AUGAAGCGCG GGUAAACGGC GGGAGUAACU AUGACUCUCU UAAGGUAGCC AAAUGCCUCG UCAUCUAAUU AGUGACGCGC AUGAAUGGAU GAACGAGAUU CCCACUGUCC CUACCUACUA UCCAGCGAAA CCACAGCCAA GGGAACGGGC UUGGCGGAAU CAGCGGGGAA AGAAGACCCU GUUGAGCUUG ACUCUAGUCU GGCACGGUGA AGAGACAUGA GAGGUGUAGA AUAAGUGGGA GGCCCGGGCC GCCGGUGAAA UACCACUACU CUGAUCGUUU UUUCACUGAC CCGGUGAGGC GGGGGGGCGA GCCGGGCUCU CGCUUCUGGC GCCAAGCGCC CGGCCGGCCG GGCGCGACCC GCUCCGGGGA CAGUGCCAGG UGGGGAGUUU GACUGGGGCG GUACACCUGU CAAACGGUAA CGCAGGUGUC CUAAGGCGAG CUCAGGGAGG ACAGAAACCU CCCGUGGAGC AGAAGGGCAA AAGCUCGCUU GAUCUUGAUU UUCAGUACGA AUACAGACCG UGAAAGCGGG GCCUCACGAU CCUUCUGACC UUUUGGGUUU UAAGCAGGAG GUGUCAGAAA AGUUACCACA GGGAUAACUG GCUUGUGGCG GCCAAGCGUU CAUAGCGACG UCGCUUUUUG AUCCUUCGAU GUCGGCUCUU CCUAUCAUUG UGAAGCAGAA UUCACCAAGC GUUGGAUUGU UCACCCACUA AUAGGGAACG UGAGCUGGGU UUAGACCGUC GUGAGACAGG UUAGUUUUAC CCUACUGAUG AUGUGUUGUU GCCAUGGUAA UCCUGCUCAG UACGAGAGGA ACCGCAGGUU CAGACAUUUG GUGUAUGUGC UUGGCUGAGG AGCCAAUGGG GCGAAGCUAC CAUCUGUGGG AUUAUGACUG AACGCCUCUA AGUCAGAAUC CCGCCCAGGC GGAACGAUAG CGCCGGAGCC UCGGUUGGCC UCGGAUAGCC GGUCCCCCGC CGGGGUCCGG UGCGGAGAGC CCUUCGUCCC GGGAAACGGG GCGGCCGGAA AGGGGGCCGC CCUCUCGCCC GUCACGCACC GCACGUUCGU GGGGAACCUG GCGCUAAACC AUUCGUAGAC GACCUGCUUC UGGGUCGGGG UUUCGUACGU AGCAGAGCAG CUGCUGCGAU CUAUUGAAAG UCAGCCCUCG ACACAAGGGU UUGU
MassTheoretical: 1.177577 MDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #41: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUACGGCC AUACCACCCU GAACGCGCCC GAUCUCGUCU GAUCUCGGAA GCUAAGCAGG GUCGGGCCUG GUUAGUACUU GGAUGGGAGA CCGCCUGGGA AUACCGGGUG CUGUAGGCUU
MassTheoretical: 38.691914 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #42: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAUC AUCGACACUU CGAACGCACU UGCGGCCCCG GGUUCCUCCC GGGGCUACGC CUGUCUGAGC GUCGCU
MassTheoretical: 50.143648 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #43: protein, Ribosomal protein L8

ProteinName: Ribosomal protein L8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.088863 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #44: protein, uL3

ProteinName: uL3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.107977 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #45: protein, uL4

ProteinName: uL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.727559 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #46: protein, 60S ribosomal protein L6

ProteinName: 60S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.028336 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #47: protein, uL30

ProteinName: uL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.201836 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #48: protein, uL6

ProteinName: uL6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.871418 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #49: protein, eL13

ProteinName: eL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.331723 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #50: protein, Ribosomal protein L14

ProteinName: Ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.870549 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #51: protein, Ribosomal protein L15

ProteinName: Ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.207285 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #52: protein, uL13

ProteinName: uL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.533299 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #53: protein, uL22

ProteinName: uL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.444221 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #54: protein, eL18

ProteinName: eL18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.699688 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #55: protein, eL19

ProteinName: eL19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.535281 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #56: protein, eL20

ProteinName: eL20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.827561 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #57: protein, eL21

ProteinName: eL21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.609988 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #58: protein, eL22

ProteinName: eL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.813015 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #59: protein, Ribosomal protein L23

ProteinName: Ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.892505 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #60: protein, eL24

ProteinName: eL24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.825111 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #61: protein, uL23

ProteinName: uL23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.768246 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #62: protein, Ribosomal protein L26

ProteinName: Ribosomal protein L26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.303363 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #63: protein, 60S ribosomal protein L27

ProteinName: 60S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.835831 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #64: protein, uL15

ProteinName: uL15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.620561 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #65: protein, eL29

ProteinName: eL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.931625 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #66: protein, eL30

ProteinName: eL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.807065 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #67: protein, eL31

ProteinName: eL31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.494938 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #68: protein, eL32

ProteinName: eL32CD59 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.898932 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #69: protein, eL33

ProteinName: eL33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.580809 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #70: protein, eL34

ProteinName: eL34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.326074 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #71: protein, uL29

ProteinName: uL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.566599 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #72: protein, 60S ribosomal protein L36

ProteinName: 60S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.263834 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #73: protein, Ribosomal protein L37

ProteinName: Ribosomal protein L37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.111032 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #74: protein, eL38

ProteinName: eL38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.238948 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #75: protein, eL39

ProteinName: eL39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.455775 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #76: protein, eL40

ProteinName: eL40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.69979 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #77: protein, eL41

ProteinName: eL41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #78: protein, eL42

ProteinName: eL42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.476973 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #79: protein, eL43

ProteinName: eL43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.29935 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #80: protein, eL28

ProteinName: eL28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.783614 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #81: protein, uL10

ProteinName: uL10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.380504 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #82: protein, Ribosomal protein L12

ProteinName: Ribosomal protein L12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.847619 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #83: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUCCGUAG UGUAGCGGUU AUCACGUUCG CCUAACACGC GAAAGGUCCU CGGUUCGAAA CCGGGCGGAA ACACCA
MassTheoretical: 24.436551 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #84: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAAUCAAAG UUUGAGCUCA AAA
MassTheoretical: 7.387504 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #85: protein, Ribosomal protein L11

ProteinName: Ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.288465 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #86: protein, eL8

ProteinName: eL8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.221516 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #87: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.481828 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #88: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.643057 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #89: protein, nascent chain

ProteinName: nascent chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.581727 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #90: protein, uL1

ProteinName: uL1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.879422 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #91: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 300 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #92: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #93: ligand, IRON/SULFUR CLUSTER

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

+
Component #94: ligand, water

LigandName: water / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
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: 1.79 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: 71954
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
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