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- EMDB-4476: Structure of tmRNA SmpB bound in A site of E. coli 70S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-4476
TitleStructure of tmRNA SmpB bound in A site of E. coli 70S ribosome
Map data
SampletmRNA SmpB bound in A site of E. coli 70S ribosome
  • 70S ribosomeRibosome
  • tmRNA-SmpB, nascent peptide, mRNA, P-site tRNA, E-site tRNA
  • (nucleic-acidNucleic acid) x 7
  • SsrA-binding protein
  • Nascent peptide
  • (50S ribosomal protein ...) x 31
  • (30S ribosomal protein ...) x 20
  • (ligand) x 3
Function / homology
Function and homology information


trans-translation-dependent protein tagging / trans-translation / mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / transcription antitermination ...trans-translation-dependent protein tagging / trans-translation / mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / transcription antitermination / translation repressor activity / mature ribosome assembly / negative regulation of translational initiation / translational initiation / polysomal ribosome / ribosome assembly / translational termination / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / maintenance of translational fidelity / DNA-binding transcription repressor activity / ribosomal small subunit assembly / regulation of cell growth / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / cytoplasmic translation / large ribosomal subunit rRNA binding / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / small ribosomal subunit / regulation of translation / protein-DNA complex / regulation of mRNA stability / response to radiation / negative regulation of translation / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / cytosol
Ribosomal protein S2, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site ...Ribosomal protein S2, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L2, domain 3 / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / K homology domain-like, alpha/beta / Ribosomal protein L2, domain 2 / 30S ribosomal protein S17 / Translation protein, beta-barrel domain superfamily / Ribosomal protein L15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L13 / Ribosomal protein L13, bacterial-type / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L30, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein L11, bacterial-type / Translation protein SH3-like domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L9/RNase H1, N-terminal / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S11, bacterial-type / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S19, bacterial-type / Ribosomal protein L21-like / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Small protein B / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L25 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L25, short-form / Ribosomal protein L11, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / SsrA-binding protein, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal
50S ribosomal protein L21 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / SsrA-binding protein / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 ...50S ribosomal protein L21 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / SsrA-binding protein / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 30S ribosomal protein S16 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 50S ribosomal protein L25 / 30S ribosomal protein S2 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 50S ribosomal protein L27 / 30S ribosomal protein S20 / 50S ribosomal protein L15 / 30S ribosomal protein S9 / 50S ribosomal protein L30 / 50S ribosomal protein L13 / 50S ribosomal protein L22 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L10 / 30S ribosomal protein S18 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L28 / 50S ribosomal protein L31 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 50S ribosomal protein L2
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsRae CD
CitationJournal: Science / Year: 2019
Title: How a circularized tmRNA moves through the ribosome.
Authors: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan /
Abstract: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo- ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.
Validation ReportPDB-ID: 6q97

SummaryFull reportAbout validation report
History
DepositionDec 17, 2018-
Header (metadata) releaseMar 13, 2019-
Map releaseMar 13, 2019-
UpdateMar 13, 2019-
Current statusMar 13, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q97
  • Surface level: 0.05
  • 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_4476.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 380 pix.
= 406.6 Å
1.07 Å/pix.
x 380 pix.
= 406.6 Å
1.07 Å/pix.
x 380 pix.
= 406.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.28233367 - 0.50819826
Average (Standard dev.)0.0013381676 (±0.013090238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 406.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z406.600406.600406.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.2820.5080.001

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Supplemental data

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Sample components

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Entire tmRNA SmpB bound in A site of E. coli 70S ribosome

EntireName: tmRNA SmpB bound in A site of E. coli 70S ribosome / Number of components: 66

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Component #1: protein, tmRNA SmpB bound in A site of E. coli 70S ribosome

ProteinName: tmRNA SmpB bound in A site of E. coli 70S ribosome / Recombinant expression: No

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Component #2: cellular-component, 70S ribosome

Cellular-componentName: 70S ribosomeRibosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, tmRNA-SmpB, nascent peptide, mRNA, P-site tRNA, E-site tRNA

ProteinName: tmRNA-SmpB, nascent peptide, mRNA, P-site tRNA, E-site tRNA
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 23S ribosomal RNA

nucleic acidName: 23S 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 GGGUCAACCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGG(PSU)GCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG CGAAGGUGUG CUGUGAGGCA UGCUGGAGGU AUCAGAAGUG CGAAUGCUGA CAUAAGUAAC GAUAAAGCGG GUGAAAAGCC CGCUCGCCGG AAGACCAAGG GUUCCUGUCC AACGUUAAUC GGGGCAGGGU GAGUCGACCC CUAAGGCGAG GCCGAAAGGC GUAGUCGAUG GGAAACAGGU UAAUAUUCCU GUACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGCGU GAUGACGAGG CACUACGGUG CUGAAGCAAC AAAUGCCCUG CUUCCAGGAA AAGCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUAA CUUCGGGAGA AGGCACGCUG AUAUGUAGGU GAGGUCCCUC GCGGAUGGAG CUGAAAUCAG UCGAAGAUAC CAGCUGGCUG CAACUGUUUA UUAAAAACAC AGCACUGUGC AAACACGAAA GUGGACGUAU ACGGUGUGAC GCCU(2MG)CCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG (PSU)AAC(3TD)A(PSU)AAC GGUCCUAAGG UAGCGAAA(5MU)U CCUUGUCGGG UAAGUUCCGA C(5MC)UGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUG(6MZ) AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGU(G7M)A ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUGGAGC CGACCUUGAA AUACCACCCU UUAAUGUUUG 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 CAGU(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: 941.526438 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: nucleic-acid, 16S ribosomal RNA

nucleic acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC 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 GCAGCC(7MG)CGG 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 CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUCA
MassTheoretical: 497.405969 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: nucleic-acid, 5S ribosomal RNA

nucleic acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCAU
MassTheoretical: 38.79009 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, SsrA-binding protein

ProteinName: SsrA-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.638166 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Nascent peptide

ProteinName: Nascent peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.008194 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: nucleic-acid, tRNA-Met

nucleic acidName: tRNA-Met / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCUACGUAG CUCAGUUGGU UAGAGCACAU CACUCAUAAU GAUGGGGUCA CAGGUUCGAA UCCCGUCGUA GCCACCA
MassTheoretical: 24.728689 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUGGUC
MassTheoretical: 1.892173 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.592166 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.672418 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.981147 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.090395 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.919411 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.592823 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.548383 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #28: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.993051 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #29: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.66156 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #30: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.208054 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #31: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #32: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.275498 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #33: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #34: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.826881 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #35: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.223367 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #36: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #37: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.131992 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #38: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.057179 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #39: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #40: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #41: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.320338 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #42: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.072867 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #43: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.248994 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #44: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #45: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.475037 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #46: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.125993 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #47: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #48: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #49: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.397688 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #50: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.254041 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #51: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #52: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.683053 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #53: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.738911 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #54: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.475364 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #55: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.072543 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #56: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.136495 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #57: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #58: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.606768 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #59: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.349939 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #60: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.50619 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #61: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.392844 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #62: nucleic-acid, transfer-messenger RNA (tmRNA)

nucleic acidName: transfer-messenger RNA (tmRNA) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGGGCUGAUU CUGGAUUCGA CGGGAUUUGC GAAACCCAAG GUGCAUGCCG AGGGGCGGUU GGCCUCGUAA AAAGCCGCAA AAAAUAGUCG CAAACGACGA AAGCUACGCU UUAGCAGCUU AAUAACCUGC UUAGAGCCCU CUCUCCCUAG CCUCCGCUCU UAGGACGGGG ...Sequence:
GGGGCUGAUU CUGGAUUCGA CGGGAUUUGC GAAACCCAAG GUGCAUGCCG AGGGGCGGUU GGCCUCGUAA AAAGCCGCAA AAAAUAGUCG CAAACGACGA AAGCUACGCU UUAGCAGCUU AAUAACCUGC UUAGAGCCCU CUCUCCCUAG CCUCCGCUCU UAGGACGGGG AUCAAGAGAG GUCAAACCCA AAAGAGAUCG CGUGGAAGCC CUGCCUGGGG UUGAAGCGUU AAAACUUAAU CAGGCUAGUU UGUUAGUGGC GUGUCCGUCC GCAGCUGGCA AGCGAAUGUA AAGACUGACU AAGCAUGUAG UACCGAGGAU GUAGGAAUUU CGGACGCGGG UUCAACUCCC GCCAGCUCCA CCA
MassTheoretical: 117.214266 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #63: nucleic-acid, tRNA-Val

nucleic acidName: tRNA-Val / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGUCCGUAG CUCAGUUGGU UAGAGCACCA CCUUGACAUG GUGGGGGUCG GUGGUUCGAG UCCACUCGGA CGCACCA
MassTheoretical: 24.823707 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #64: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 439 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #65: ligand, ZINC ION

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

+
Component #66: ligand, water

LigandName: water / Number of Copies: 2 / 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: 44 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: 47776
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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