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- EMDB-12936: Cryo-EM structure of 70S ribosome stalled with TnaC peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-12936
TitleCryo-EM structure of 70S ribosome stalled with TnaC peptide
Map data
Sample70S ribosomeRibosome:
(nucleic-acidNucleic acid) x 5 / (30S ribosomal protein ...) x 20 / (50S ribosomal protein ...) x 29 / TnaC / (ligand) x 4
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / negative regulation of translational initiation / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / DNA-templated transcription, termination / maintenance of translational fidelity / positive regulation of translational fidelity / response to reactive oxygen species / regulation of cell growth / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / ribosome binding / large ribosomal subunit / ribosomal large subunit assembly / regulation of translation / 5S rRNA binding / response to radiation / small ribosomal subunit / regulation of mRNA stability / cytosolic small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein S21 superfamily ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L34, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L34 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L6, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein S3, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L20 / L28p-like / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein L30, bacterial-type / Ribosomal L32p protein family / Ribosomal protein L16 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20, C-terminal / Ribosomal protein L20
Similarity search - Domain/homology
50S ribosomal protein L30 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 50S ribosomal protein L21 ...50S ribosomal protein L30 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 30S ribosomal protein S4 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 30S ribosomal protein S5 / 50S ribosomal protein L9 / 30S ribosomal protein S3 / 50S ribosomal protein L28 / 50S ribosomal protein L31 / 30S ribosomal protein S11 / 30S ribosomal protein S10 / 30S ribosomal protein S16 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 30S ribosomal protein S2 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSu T / Kudva R / Becker T / Berninghausen O / Heijne G / Cheng J / Beckmann R
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
Authors: Ting Su / Renuka Kudva / Thomas Becker / Robert Buschauer / Tobias Komar / Otto Berninghausen / Gunnar von Heijne / Jingdong Cheng / Roland Beckmann /
Abstract: In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation- ...In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation-termination by the UGA-specific decoding release factor 2 (RF2) is inhibited at the UGA stop codon of stalled TnaC-ribosome-nascent chain complexes has so far been ambiguous. This study presents cryo-EM structures for ribosomes stalled by TnaC in the absence and presence of RF2 at average resolutions of 2.9 and 3.5 Å, respectively. Stalled TnaC assumes a distinct conformation composed of two small α-helices that act together with residues in the peptide exit tunnel (PET) to coordinate a single L-Trp molecule. In addition, while the peptidyl-transferase center (PTC) is locked in a conformation that allows RF2 to adopt its canonical position in the ribosome, it prevents the conserved and catalytically essential GGQ motif of RF2 from adopting its active conformation in the PTC. This explains how translation of the TnaC peptide effectively allows the ribosome to function as a L-Trp-specific small-molecule sensor that regulates the tnaCAB operon.
History
DepositionMay 13, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oiz
  • Surface level: 0.025
  • 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_12936.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 368 pix.
= 398.912 Å
1.08 Å/pix.
x 368 pix.
= 398.912 Å
1.08 Å/pix.
x 368 pix.
= 398.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.2575581 - 0.45429444
Average (Standard dev.)0.00014541912 (±0.013086243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 398.912 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z398.912398.912398.912
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.2580.4540.000

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Supplemental data

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Sample components

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Entire 70S ribosome

EntireName: 70S ribosomeRibosome / Number of Components: 60

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Component #1: protein, 70S ribosome

ProteinName: 70S ribosomeRibosome / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #2: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA ...Sequence:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA AUACCGCAUA ACGUCGCAAG ACCAAAGAGG GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCCGCGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC GGCGUGGCUU CCGGAGCUAA CGCGUUAAGU CGACCGCCUG GGGAGUACGG CCGCAAGGUU AAAACUCAAA UGAAUUGACG GGGGCCCGCA CAAGCGGUGG AGCAUGUGGU UUAAUUCGAU (2MG)(5MC)AACGCGAA GAACCUUACC UGGUCUUGAC AUCCACGGAA GUUUUCAGAG AUGAGAAUGU GCCUUCGGGA ACCGUGAGAC AGGUGCUGCA UGGCUGUCGU CAGCUCGUGU UGUGAAAUGU UGGGUUAAGU CCCGCAACGA GCGCAACCCU UAUCCUUUGU UGCCAGCGGU CCGGCCGGGA ACUCAAAGGA GACUGCCAGU GAUAAACUGG AGGAAGGUGG GGAUGACGUC AAGUCAUCAU G(2MG)CCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCGACCUC GCGAGAGCAA GCGGACCUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAGAAUG CCACGGUGAA UACGUUCCCG GGCCUUGUAC ACACCG(4OC)CCG U(5MC)ACACCAUG GGAGUGGGUU GCAAAAGAAG UAGGUAGCUU AACCUUCGGG AGGGCGCUUA CCACUUUGUG AUUCAUGACU GGGGUGAAGU CG(UR3)AACAAGG UAACCGUAGG (2MG)G(MA6)(MA6)CCUGCG GUUGGAUCA
MassTheoretical: 492.576094 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #7: protein, 30S ribosomal protein S6, fully modified isoform

ProteinName: 30S ribosomal protein S6, fully modified isoformRibosome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.727512 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.871959 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.768157 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #15: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #23: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU ...Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAU(1MG)(PSU)(5MU)GAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGG(PSU)GCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCGUCGAGUC GGCCUGCGCG GAAGAUGUAA CGGGGCUAAA CCAUGCACCG AAGCUGCGGC AGCGACGCGC GUUGUUGGGU AGGGGAGCGU UCUGUAAGCC UGCGAAGGUG UGCUGUGAGG CAUGCUGGAG GUAUCAGAAG UGCGAAUGCU GACAUAAGUA ACGAUAAAGC GGGUGAAAAG CCCGCUCGCC GGAAGACCAA GGGUUCCUGU CCAACGUUAA UCGGGGCAGG GUGAGUCGAC CCCUAAGGCG AGGCCGAAAG GCGUAGUCGA UGGGAAACAG GUUAAUAUUC CUGUACUUGG UGUUACUGCG AAGGGGGGAC GGAGAAGGCU AUGUUGGCCG GGCGACGGUU GUCCCGGUUU AAGCGUGUAG GCUGGUUUUC CAGGCAAAUC CGGAAAAUCA AGGCUGAGGC GUGAUGACGA GGCACUACGG UGCUGAAGCA ACAAAUGCCC UGCUUCCAGG AAAAGCCUCU AAGCAUCAGG UAACAUCAAA UCGUACCCCA AACCGACAC(6MZ) GGUGGUCAGG UAGAGAAUAC CAAGGCGCUU GAGAGAACUC GGGUGAAGGA ACUAGGCAAA AUGGUGCCGU AACUUCGGGA GAAGGCACGC UGAUAUGUAG GUGAGGUCCC UCGCGGAUGG AGCUGAAAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCU(2MG)CCC GGUGCCGGAA GGUUAAUUGA UGGGGUUAGC GCAAGCGAAG CUCUUGAUCG AAGCCCCGGU AAACGGCGGC CG(PSU)AAC(3TD)A(PSU)A ACGGUCCUAA GGUAGCGAAA (5MU)UCCUUGUCG GGUAAGUUCC GAC(5MC)UGCACG AAUGGCGUAA UGAUGGCCAG GCUGUCUCCA CCCGAGACUC AGUGAAAUUG AACUCGCUGU G(6MZ)AGAUGCAG UGUACCCGCG GCAAGACGGA AAGACCCCGU (G7M)AACCUUUAC UAUAGCUUGA CACUGAACAU AUGUUCUAAC GUUGACCCGU AAUCCGGGUU GCGGACAGUG UCUGGUGGGU AGUUUGACUG (OMG)GGCGGUCUC CUCCUAAAGA GUAACGGAGG AGCACGAAGG UUGGCUAAUC CUGGUCGGAC AUCAGGAGGU UAGUGCAAUG GCAUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCG(2MG)GGAUA ACAGGC(PSU)GAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCA(OMC)CU CG(2MA)(PSU)GUCGGC UCAUCACAUC CUGGGGCUGA AGUAGGUCCC AAGGGUAUGG C(OMU)GUUCGCCA UUUAAAGUGG UACGCGAGC(PSU) GGGUUUAGAA CGUCGUGAGA CAG(PSU)(PSU)CGGUC CCUAUCUGCC GUGGGCGCUG GAGAACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACUGCCCGGU AGCUAAAUGC GGAAGAGAUA AGUGCUGAAA GCAUCUAAGC ACGAAACUUG CCCCGAGAUG AGUUCUCCCU GACCCUUUAA GGGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCU
MassTheoretical: 893.064562 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #24: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCA
MassTheoretical: 38.483926 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #25: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #26: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.291562 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #27: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #28: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #29: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #30: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #31: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #32: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #33: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #34: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #35: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #36: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #37: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #38: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #39: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #40: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #41: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #42: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #43: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #44: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #45: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #46: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #47: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #48: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #49: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #50: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #51: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #52: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #53: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

+
Component #54: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CCCUGA
MassTheoretical: 1.851165 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #55: protein, TnaC

ProteinName: TnaC / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.974223 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #56: nucleic-acid, tRNA

nucleic acidName: tRNATransfer RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGGCACGUAG CGCAGCGGUA GCGCACCGUC AUGGGGUGUC GGGGGUCGGA GG(5MU)UCAAAUC CUCUCGUGCC GACCA
MassTheoretical: 24.279453 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #57: ligand, PAROMOMYCIN

LigandName: PAROMOMYCIN / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.615628 kDa

+
Component #58: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 308 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #59: ligand, TRYPTOPHAN

LigandName: TRYPTOPHAN / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.204225 kDa

+
Component #60: ligand, ZINC ION

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

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
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: 28 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 459171
3D reconstructionResolution: 2.9 Å / Resolution Method: FSC 0.143 CUT-OFF / Euler angles: Relion

-
Atomic model buiding

Output model

+
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