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- EMDB-12693: Cryo-EM structure of an Escherichia coli TnaC-ribosome complex st... -

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Basic information

Entry
Database: EMDB / ID: EMD-12693
TitleCryo-EM structure of an Escherichia coli TnaC-ribosome complex stalled in response to L-tryptophan
Map data
Sample70S ribosome stalled during translation of TnaC with Pro24 in the P-site.
  • 30S subunitProkaryotic small ribosomal subunit
  • 50S subunitProkaryotic large ribosomal subunit
  • P-site tRNA-Pro - TnaC nascent chain
  • mRNAMessenger RNA
  • (nucleic-acidNucleic acid) x 5
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • Tryptophanase leader peptide
  • (ligand) x 4
Function / homology
Function and homology information


transcriptional attenuation by ribosome / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity ...transcriptional attenuation by ribosome / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / four-way junction DNA binding / negative regulation of translational initiation / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / translational initiation / polysomal ribosome / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / ribosome assembly / endodeoxyribonuclease activity / DNA-templated transcription, termination / positive regulation of translational fidelity / maintenance of translational fidelity / response to reactive oxygen species / regulation of cell growth / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / regulation of mRNA stability / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal large subunit assembly / ribosome biogenesis / response to radiation / 5S rRNA binding / small ribosomal subunit / 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 / cytosol
Similarity search - Function
Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Ribosomal protein S21 signature. / Ribosomal protein S21, conserved site / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Ribosomal protein S21 signature. / Ribosomal protein S21, conserved site / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / 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 / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 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, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L5, bacterial-type / Ribosomal protein L19 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 L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L20 signature. / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 / 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 L34 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal L28 family / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S18 signature. / Ribosomal protein S18, conserved site / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / L28p-like / Ribosomal L32p protein family / Ribosomal proteins 50S L24/mitochondrial 39S L24
Similarity search - Domain/homology
50S ribosomal protein L21 / 30S ribosomal protein S5 / 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 / 30S ribosomal protein S5 / 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 L2 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 30S ribosomal protein S3 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 30S ribosomal protein S2 / 50S ribosomal protein L32 / Tryptophanase leader peptide / 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 L28 / 50S ribosomal protein L29 / 50S ribosomal protein L31 / 50S ribosomal protein L33 / 30S ribosomal protein S20 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
Authorsvan der Stel AX / Gordon ER / Sengupta A / Martinez AK / Klepacki D / Perry TN / Herrero del Valle A / Vazquez-Laslop N / Sachs MS / Cruz-Vera LR / Innis CA
Funding support France, United States, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)724040 France
National Science Foundation (NSF, United States)MCB-1158271 United States
National Science Foundation (NSF, United States)MCB-1951405 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM47498 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling.
Authors: Anne-Xander van der Stel / Emily R Gordon / Arnab Sengupta / Allyson K Martínez / Dorota Klepacki / Thomas N Perry / Alba Herrero Del Valle / Nora Vázquez-Laslop / Matthew S Sachs / Luis R ...Authors: Anne-Xander van der Stel / Emily R Gordon / Arnab Sengupta / Allyson K Martínez / Dorota Klepacki / Thomas N Perry / Alba Herrero Del Valle / Nora Vázquez-Laslop / Matthew S Sachs / Luis R Cruz-Vera / C Axel Innis /
Abstract: Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive ...Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.
History
DepositionMar 29, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 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: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o19
  • Surface level: 0.01
  • 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_12693.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 408 pix.
= 370.056 Å
0.91 Å/pix.
x 408 pix.
= 370.056 Å
0.91 Å/pix.
x 408 pix.
= 370.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.907 Å
Density
Contour LevelBy AUTHOR: 0.0075 / Movie #1: 0.01
Minimum - Maximum-0.019225864 - 0.09390483
Average (Standard dev.)0.00042900097 (±0.004900676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 370.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9070.9070.907
M x/y/z408408408
origin x/y/z0.0000.0000.000
length x/y/z370.056370.056370.056
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS408408408
D min/max/mean-0.0190.0940.000

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Supplemental data

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Segmentation: #1

Fileemd_12693_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map 1 of E. coli 70S ribosome stalled on...

Fileemd_12693_half_map_1.map
AnnotationHalf-map_1 of E. coli 70S ribosome stalled on the TnaC peptide in complex with L-tryptophan
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map 2 of E. coli 70S ribosome stalled on...

Fileemd_12693_half_map_2.map
AnnotationHalf-map_2 of E. coli 70S ribosome stalled on the TnaC peptide in complex with L-tryptophan
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 70S ribosome stalled during translation of TnaC with Pro24 in the...

EntireName: 70S ribosome stalled during translation of TnaC with Pro24 in the P-site.
Details: mRNA was translated in vitro using an S30 extract-based system, to obtain a stalled 70S:TnaC:tRNA-Pro:mRNA:L-Trp complex.
Number of Components: 64

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Component #1: protein, 70S ribosome stalled during translation of TnaC with Pro...

ProteinName: 70S ribosome stalled during translation of TnaC with Pro24 in the P-site.
Details: mRNA was translated in vitro using an S30 extract-based system, to obtain a stalled 70S:TnaC:tRNA-Pro:mRNA:L-Trp complex.
Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #2: protein, 30S subunit

ProteinName: 30S subunitProkaryotic small ribosomal subunit / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #3: protein, 50S subunit

ProteinName: 50S subunitProkaryotic large ribosomal subunit / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #4: protein, P-site tRNA-Pro - TnaC nascent chain

ProteinName: P-site tRNA-Pro - TnaC nascent chain / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #5: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)
Source (engineered)Expression System: synthetic construct (others)

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Component #6: nucleic-acid, Ribosomal RNA 16S

nucleic acidName: Ribosomal RNA 16S / 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(G7M)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: 497.404969 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #7: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #8: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #9: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #10: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #11: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.727512 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #12: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #13: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #14: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #15: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #16: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #17: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.814249 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #18: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #19: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.677637 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #20: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #21: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #22: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #23: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #24: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #25: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #26: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #27: nucleic-acid, Ribosomal RNA 23S

nucleic acidName: Ribosomal RNA 23S / 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 GGGUCACUUA CCAACCCGAU GCAAACUGCG AAUACCGGAG AAUGUUAUCA CGGGAGACAC ACGGCGGG(PSU)G CUAACGUCCG UCGUGAAGAG GGAAACAACC CAGACCGCCA GCUAAGGUCC CAAAGUCAUG GUUAAGUGGG AAACGAUGUG GGAAGGCCCA GACAGCCAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAAAGCGUAA UAGCUCACUG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUCUGUAAG CCUGCGAAGG UGUGCUGUGA GGCAUGCUGG AGGUAUCAGA AGUGCGAAUG CUGACAUAAG UAACGAUAAA GCGGGUGAAA AGCCCGCUCG CCGGAAGACC AAGGGUUCCU GUCCAACGUU AAUCGGGGCA GGGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGAAGG CUAUGUUGGC CGGGCGACGG UUGUCCCGGU UUAAGCGUGU AGGCUGGUUU UCCAGGCAAA UCCGGAAAAU CAAGGCUGAG GCGUGAUGAC GAGGCACUAC GGUGCUGAAG CAACAAAUGC CCUGCUUCCA GGAAAAGCCU CUAAGCAUCA GGUAACAUCA AAUCGUACCC CAAACCGACA C(6MZ)GGUGGUCA GGUAGAGAAU ACCAAGGCGC UUGAGAGAAC UCGGGUGAAG GAACUAGGCA AAAUGGUGCC GUAACUUCGG GAGAAGGCAC GCUGAUAUGU AGGUGAGGUC CCUCGCGGAU GGAGCUGAAA UCAGUCGAAG AUACCAGCUG GCUGCAACUG UUUAUUAAAA ACACAGCACU GUGCAAACAC GAAAGUGGAC GUAUACGGUG UGACGCCU(2MG)C CCGGUGCCGG AAGGUUAAUU GAUGGGGUUA GCGCAAGCGA AGCUCUUGAU CGAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGAC(5MC)UGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGAC UCAGUGAAAU UGAACUCGCU GUG(6MZ)AGAUGC AGUGUACCCG CGGCAAGACG GAAAGACCCC GU(G7M)AACCUUU ACUAUAGCUU GACACUGAAC AUUGAGCCUU GAUGUGUAGG AUAGGUGGGA GGCUUUGAAG UGUGGACGCC AGUCUGCAUG GAGCCGACCU UGAAAUACCA CCCUUUAAUG UUUGAUGUUC UAACGUUGAC CCGUAAUCCG GGUUGCGGAC AGUGUCUGGU GGGUAGUUUG ACUG(OMG)GGCGG UCUCCUCCUA AAGAGUAACG GAGGAGCACG AAGGUUGGCU AAUCCUGGUC GGACAUCAGG AGGUUAGUGC AAUGGCAUAA GCCAGCUUGA CUGCGAGCGU GACGGCGCGA GCAGGUGCGA AAGCAGGUCA UAGUGAUCCG GUGGUUCUGA AUGGAAGGGC CAUCGCUCAA CGGAUAAAAG GUACUCCG(2MG)G GAUAACAGGC (PSU)GAUACCGCC CAAGAGUUCA UAUCGACGGC GGUGUUUGGC A(OMC)CUCG(2MA)(PSU)GU CGGCUCAUCA CAUCCUGGGG CUGAAGUAGG UCCCAAGGGU AUGGC(OMU)GUUC GCCAUUUAAA GUGGUACGCG AGC(PSU)GGGUUU AGAACGUCGU GAGACAG(PSU)(PSU)C GGUCCCUAUC UGCCGUGGGC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACUGCC CGGUAGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAAGGGUCC UGAAGGAACG UUGAAGACGA CGACGUUGAU AGGCCGGGUG UGUAAGCGCA GCGAUGCGUU GAGCUAACCG GUACUAAUGA ACCGUGAGGC UUAACCU
MassTheoretical: 939.60725 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #28: nucleic-acid, Ribosomal RNA 5S

nucleic acidName: Ribosomal RNA 5S / 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 K-12 (bacteria)

+
Component #29: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #30: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.291562 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #31: 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)

+
Component #32: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #33: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #34: 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 #35: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.887117 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #36: 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 #37: 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 #38: 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 #39: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.327261 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #40: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #41: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #42: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #43: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #44: 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 #45: 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 #46: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #47: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #48: 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 #49: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #51: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #52: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #53: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #54: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #55: 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 #56: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #57: 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 #58: protein, Tryptophanase leader peptide

ProteinName: Tryptophanase leader peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.073354 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #59: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCCCGU
MassTheoretical: 2.172347 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #60: nucleic-acid, P-site tRNA-Pro

nucleic acidName: P-site tRNA-Pro / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGGUGAUUGG CGCAGCCUGG UAGCGCACUU CGUUCGGGAC GAAGGGGUCG GAGGUUCGAA UCCUCUAUCA CCGACCA
MassTheoretical: 24.846746 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #61: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 170 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #62: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #63: ligand, TRYPTOPHAN

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

+
Component #64: ligand, water

LigandName: water / Number of Copies: 793 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/mL
Buffer solution: All buffers used during the preparation contained 2 mM L-tryptophan.
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 45000.0 X (nominal), 55127.0 X (calibrated) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: -1000.0 - -2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 9170

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 93588
3D reconstructionSoftware: RELION / Resolution: 2.9 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 6TBV
Output model

+
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