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- EMDB-11420: E. coli 70S-RNAP expressome complex in collided state without NusG -

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Basic information

Entry
Database: EMDB / ID: EMD-11420
TitleE. coli 70S-RNAP expressome complex in collided state without NusG
Map data
SampleUncoupled E. coli expressome, state 1
  • 70S ribosome within the E. coli 70S-RNAP expressome complex in collided state without NusG
  • DNA-directed RNA polymerase within the E. coli 70S-RNAP expressome complex in collided state without NusG
  • synthetic mRNA and template DNA strands
  • (nucleic-acidNucleic acid) x 8
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 3
  • (ligand) x 3
Function / homology
Function and homology information


endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / ribosome assembly / ribonucleoside binding / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / DNA-templated transcription, termination ...endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / ribosome assembly / ribonucleoside binding / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / DNA-templated transcription, termination / assembly of large subunit precursor of preribosome / regulation of cell growth / response to reactive oxygen species / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / response to radiation / small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / protein dimerization activity / translation / transcription, DNA-templated / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / magnesium ion binding / RNA binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Ribosomal protein L30, conserved site / Ribosomal S11, conserved site / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Ribosomal protein L2, domain 3 / DNA-directed RNA polymerase, subunit 2 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain ...Ribosomal protein L30, conserved site / Ribosomal S11, conserved site / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Ribosomal protein L2, domain 3 / DNA-directed RNA polymerase, subunit 2 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal L18e/L15P superfamily / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein L25/L23 / 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 L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S5, N-terminal / 50S ribosomal protein uL4 / Ribosomal protein S21, conserved site / K homology domain superfamily, prokaryotic type / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein L9/RNase H1, N-terminal / DNA-directed RNA polymerase, subunit beta-prime / S15/NS1, RNA-binding / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA polymerase, alpha subunit, C-terminal / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Zinc-binding ribosomal protein / DNA-directed RNA polymerase, alpha subunit / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / RNA polymerase, N-terminal / Ribosomal protein L28/L24 / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L2, C-terminal / Ribosomal protein L35 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Ribosomal protein L9, C-terminal / 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 / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L18e/L15P
50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L9 / 50S ribosomal protein L17 / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 ...50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L9 / 50S ribosomal protein L17 / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / DNA-directed RNA polymerase subunit alpha / 50S ribosomal protein L30 / 50S ribosomal protein L21 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 30S ribosomal protein S13 / 50S ribosomal protein L29 / 30S ribosomal protein S11 / 30S ribosomal protein S5 / 50S ribosomal protein L36 / 30S ribosomal protein S18 / 30S ribosomal protein S12 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S4 / 50S ribosomal protein L28 / 30S ribosomal protein S9 / 30S ribosomal protein S15 / 30S ribosomal protein S21 / 30S ribosomal protein S16 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 30S ribosomal protein S6
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWebster MW / Takacs M / Weixlbaumer A
Funding support France, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)679734 France
French National Research AgencyANR-10-LABX-0030-INRT France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
European Molecular Biology Organization (EMBO)LTF375-2019 France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Science / Year: 2020
Title: Structural basis of transcription-translation coupling and collision in bacteria.
Authors: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer /
Abstract: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.
Validation ReportPDB-ID: 6ztm

SummaryFull reportAbout validation report
History
DepositionJul 20, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ztm
  • Surface level: 0.5
  • 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_11420.map.gz / Format: CCP4 / Size: 1000 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 640 pix.
= 688. Å
1.08 Å/pix.
x 640 pix.
= 688. Å
1.08 Å/pix.
x 640 pix.
= 688. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.43392098 - 2.9811132
Average (Standard dev.)0.021395102 (±0.06815013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 688.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0751.0751.075
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z688.000688.000688.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS640640640
D min/max/mean-0.4342.9810.021

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Supplemental data

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_1.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 1 of focused refinement 4 of 4 (30S-head masked).
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_10.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: focused refinement 2 of 4 (RNAP masked).
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_11.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 1 of focused refinement 3 of 4 (30S-body masked).
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_12.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 2 of focused refinement 4 of 4 (30S-head masked).
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_13.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 1 of focused refinement 2 of 4 (RNAP masked).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_14.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 2 of focused refinement 2 of 4 (RNAP masked).
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AxesZYX

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Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_2.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: focused refinement 4 of 4 (30S-head masked).
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AxesZYX

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Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_3.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: expressome map non-composite.
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_4.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 2 of focused refinement 3 of 4 (30S-body masked).
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_5.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: composite map with local density sharpening.
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_6.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 1 of expressome refinement.
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AxesZYX

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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_7.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 2 of expressome refinement.
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_8.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: focused refinement 1 of 4 (70S masked).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_additional_9.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: focused refinement 3 of 4 (30S-body masked).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_half_map_1.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 1 of focused refinement 1 of 4 (70S masked).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: Collided E. coli expressome with intervening mRNA length...

Fileemd_11420_half_map_2.map
AnnotationCollided E. coli expressome with intervening mRNA length 34 nucleotides: half map 2 of focused refinement 1 of 4 (70S masked).
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AxesZYX

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Sample components

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Entire Uncoupled E. coli expressome, state 1

EntireName: Uncoupled E. coli expressome, state 1 / Number of components: 66

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Component #1: protein, Uncoupled E. coli expressome, state 1

ProteinName: Uncoupled E. coli expressome, state 1 / Recombinant expression: No

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Component #2: protein, 70S ribosome within the E. coli 70S-RNAP expressome comp...

ProteinName: 70S ribosome within the E. coli 70S-RNAP expressome complex in collided state without NusG
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, DNA-directed RNA polymerase within the E. coli 70S-RNAP ...

ProteinName: DNA-directed RNA polymerase within the E. coli 70S-RNAP expressome complex in collided state without NusG
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pEcrpoABC(-XH)Z

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Component #4: protein, synthetic mRNA and template DNA strands

ProteinName: synthetic mRNA and template DNA strands / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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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 AACAGGAAGC AGCUUGCUGC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGC AGCUUGCUGC 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 AUCACCUCCU UA
MassTheoretical: 499.888406 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.617455 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.197032 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.637445 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.814249 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACAAAGGAGG UAUUCAUGUU CACAUACACA UAUAUAGACA CACACAAACG GCGCGCG
MassTheoretical: 18.329033 kDa
SourceSpecies: synthetic construct (others)

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Component #27: nucleic-acid, tRNA(fmet) P-site

nucleic acidName: tRNA(fmet) P-site / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGG(4SU)GG AGCAGCCUGG (H2U)AGCUCGUCG GG(OMC)UCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.832918 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #28: nucleic-acid, Phe-NH-tRNA(Phe) A-site

nucleic acidName: Phe-NH-tRNA(Phe) A-site / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCCGGA(4SU)AG CUCAG(H2U)CGG(H2U) AGAGCAGGGG A(PSU)UGAA(MIA)A(PSU)C CCCGU(7MG)(3AU)CCU UGG(5MU)(PSU)CGAUU CCGAGUCCGG GCACCA
MassTheoretical: 24.751018 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #29: 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 ACAGAAAUCU 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 GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG UGAAGGUGUG 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 GAUCCGGGUU 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)GGA(H2U)A 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 GACUCCUUGA GAGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCUU
MassTheoretical: 941.820562 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #30: 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)

+
Component #31: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #32: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.291562 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #33: 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)

+
Component #34: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #35: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #36: 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)

+
Component #37: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #38: 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)

+
Component #39: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.994443 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #40: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.327261 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #41: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #42: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #43: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #44: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #45: 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)

+
Component #46: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #47: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #48: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (E. coli)

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

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #51: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #52: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #53: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #54: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #55: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #56: 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 #57: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #58: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.72006 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #59: nucleic-acid, Non-template DNA strand

nucleic acidName: Non-template DNA strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DT)(DC)(DA)(DG)(DT)(DA)(DC)(DG) (DT)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT) (DC)(DT)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DA)(DT)(DT)(DC)(DA)(DG)(DA)(DG)
MassTheoretical: 12.063754 kDa
SourceSpecies: synthetic construct (others)

+
Component #60: nucleic-acid, Template DNA strand

nucleic acidName: Template DNA strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DT) (DC)(DT)(DT)(DC)(DC)(DC)(DG)(DC)(DG)(DC) (DG)(DC)(DC)(DG)(DT)(DA)(DG)(DG)(DA)(DC) (DG)(DT)(DA)(DC)(DT)(DG)(DA)(DC)(DC)
MassTheoretical: 11.872596 kDa
SourceSpecies: synthetic construct (others)

+
Component #61: protein, DNA-directed RNA polymerase subunit alpha

ProteinName: DNA-directed RNA polymerase subunit alphaPolymerase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 36.55868 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #62: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 150.820875 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #63: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta'Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 155.366781 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #64: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 421 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #65: ligand, PHENYLALANINE

LigandName: PHENYLALANINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.165189 kDa

+
Component #66: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 700.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18552
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 4YBB, 6ALH
Output model

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