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- EMDB-7016: Structure of 30S (S1 depleted) ribosomal subunit and RNA polymera... -

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Entry
Database: EMDB / ID: EMD-7016
TitleStructure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex
Map data
Sample30S (S1 depleted) ribosomal subunit and RNA polymerase complex
  • 30S (S1 depleted) ribosomal subunit
  • RNA polymerase
  • nucleic-acidNucleic acid
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • (30S ribosomal protein ...) x 20
Function / homology
Function and homology information


ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / transcription, DNA-templated ...ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / transcription, DNA-templated / protein dimerization activity / mRNA binding / magnesium ion binding / DNA binding / zinc ion binding
RNA polymerase Rpb2, OB-fold / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / DNA-directed RNA polymerase, subunit 2 ...RNA polymerase Rpb2, OB-fold / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, insert domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / DNA-directed RNA polymerase, subunit beta-prime / Ribosomal protein S18, conserved site / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / RNA polymerase, alpha subunit, C-terminal / Ribosomal protein S13-like, H2TH / DNA-directed RNA polymerase beta subunit, bacterial-type / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / RNA polymerase Rpb2, domain 3 / Ribosomal protein S14, conserved site / Ribosomal protein S21, conserved site / RNA polymerase Rpb2, domain 2 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S3, C-terminal domain superfamily / RPB6/omega subunit-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S3, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 7 / RNA polymerase, RBP11-like subunit / Ribosomal protein S17/S11 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9 / RNA polymerase, alpha subunit / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S5/S7 / RNA polymerase, beta subunit, conserved site / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / Ribosomal protein S21 superfamily / RNA polymerase Rpb1, domain 3 superfamily / Ribosomal protein S14/S29 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S21 / Ribosomal protein S4/S9, N-terminal / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase, subunit omega/K/RPB6 / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid
30S ribosomal protein S10 / DNA-directed RNA polymerase subunit alpha / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / DNA-directed RNA polymerase subunit beta / 30S ribosomal protein S16 / DNA-directed RNA polymerase subunit omega / 30S ribosomal protein S12 ...30S ribosomal protein S10 / DNA-directed RNA polymerase subunit alpha / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / DNA-directed RNA polymerase subunit beta / 30S ribosomal protein S16 / DNA-directed RNA polymerase subunit omega / 30S ribosomal protein S12 / 30S ribosomal protein S7 / 30S ribosomal protein S11 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S4 / 30S ribosomal protein S9 / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / DNA-directed RNA polymerase subunit beta'
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsDemo G / Rasouly A / Vasilyev N / Loveland AB / Diaz-Avalos R / Grigorieff N / Nudler E / Korostelev AA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106105 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 United States
CitationJournal: Elife / Year: 2017
Title: Structure of RNA polymerase bound to ribosomal 30S subunit.
Authors: Gabriel Demo / Aviram Rasouly / Nikita Vasilyev / Vladimir Svetlov / Anna B Loveland / Ruben Diaz-Avalos / Nikolaus Grigorieff / Evgeny Nudler / Andrei A Korostelev /
Abstract: In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA ...In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 5, 2017-
Header (metadata) releaseOct 18, 2017-
Map releaseOct 18, 2017-
UpdateJan 1, 2020-
Current statusJan 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6awd
  • Surface level: 2
  • 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_7016.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 280 pix.
= 528.64 Å
1.89 Å/pix.
x 280 pix.
= 528.64 Å
1.89 Å/pix.
x 280 pix.
= 528.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.888 Å
Density
Contour LevelBy AUTHOR: 2 / Movie #1: 2
Minimum - Maximum-3.5762236 - 13.228021
Average (Standard dev.)-0.053800687 (±0.6797178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 528.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8881.8881.888
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z528.640528.640528.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-3.57613.228-0.054

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Supplemental data

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Sample components

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Entire 30S (S1 depleted) ribosomal subunit and RNA polymerase complex

EntireName: 30S (S1 depleted) ribosomal subunit and RNA polymerase complex
Number of components: 28

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Component #1: protein, 30S (S1 depleted) ribosomal subunit and RNA polymerase c...

ProteinName: 30S (S1 depleted) ribosomal subunit and RNA polymerase complex
Recombinant expression: No
MassTheoretical: 1.3 MDa

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Component #2: protein, 30S (S1 depleted) ribosomal subunit

ProteinName: 30S (S1 depleted) ribosomal subunit / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, RNA polymerase

ProteinName: RNA polymerase / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA ...Sequence:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA AUACCGCAUA ACGUCGCAAG ACCAAAGAGG GGGACCUUCG GGCCUCUUGC CAUCGGAUGU GCCCAGAUGG GAUUAGCUAG UAGGUGGGGU AACGGCUCAC CUAGGCGACG AUCCCUAGCU GGUCUGAGAG GAUGACCAGC CACACUGGAA CUGAGACACG GUCCAGACUC CUACGGGAGG CAGCAGUGGG GAAUAUUGCA CAAUGGGCGC AAGCCUGAUG CAGCCAUGCC GCGUGUAUGA AGAAGGCCUU CGGGUUGUAA AGUACUUUCA GCGGGGAGGA AGGGAGUAAA GUUAAUACCU UUGCUCAUUG ACGUUACCCG CAGAAGAAGC ACCGGCUAAC UCCGUGCCAG CAGCCGCGGU AAUACGGAGG GUGCAAGCGU UAAUCGGAAU UACUGGGCGU AAAGCGCACG CAGGCGGUUU GUUAAGUCAG AUGUGAAAUC CCCGGGCUCA ACCUGGGAAC UGCAUCUGAU ACUGGCAAGC UUGAGUCUCG UAGAGGGGGG UAGAAUUCCA GGUGUAGCGG UGAAAUGCGU AGAGAUCUGG AGGAAUACCG GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG AUACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAGU ACGGCCGCAA GGUUAAAACU CAAAUGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAUGCAACG CGAAGAACCU UACCUGGUCU UGACAUCCAC GGAAGUUUUC AGAGAUGAGA AUGUGCCUUC GGGAACCGUG AGACAGGUGC UGCAUGGCUG UCGUCAGCUC GUGUUGUGAA AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUUAUCCU UUGUUGCCAG CGGUCCGGCC GGGAACUCAA AGGAGACUGC CAGUGAUAAA CUGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUGGCCCU UACGACCAGG GCUACACACG UGCUACAAUG GCGCAUACAA AGAGAAGCGA CCUCGCGAGA GCAAGCGGAC CUCAUAAAGU GCGUCGUAGU CCGGAUUGGA GUCUGCAACU CGACUCCAUG AAGUCGGAAU CGCUAGUAAU CGUGGAUCAG AAUGCCACGG UGAAUACGUU CCCGGGCCUU GUACACACCG CCCGUCACAC CAUGGGAGUG GGUUGCAAAA GAAGUAGGUA GCUUAACCUU CGGGAGGGCG CUUACCACUU UGUGAUUCAU GACUGGGGUG AAGUCGUAAC AAGGUAACCG UAGGGGAACC UGCGGUUGGA UCACCUCCU
MassTheoretical: 498.725406 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: protein, DNA-directed RNA polymerase subunit alpha

ProteinName: DNA-directed RNA polymerase subunit alphaPolymerase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.33983 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 150.560562 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta'Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 151.537594 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, DNA-directed RNA polymerase subunit omega

ProteinName: DNA-directed RNA polymerase subunit omegaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.552496 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.253943 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: 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)

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Component #12: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.532088 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.669371 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: 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)

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Component #15: 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)

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Component #16: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.196988 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.388068 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: 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)

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Component #22: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: 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 #24: 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)

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Component #25: 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)

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Component #26: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.057626 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: 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)

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Component #28: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.763073 kDa
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %
Details: 2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8..

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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: 22000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1641
Details: The average electron dose 40.0 (e-/A2) represents the total dose for one collected movie.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 21123
3D reconstructionSoftware: FREALIGN / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Correlation Coefficient / Refinement space: REAL / Overall bvalue: 500
Output model

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