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- EMDB-8505: Structural Basis of Co-translational Quality Control by ArfA and ... -

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Basic information

Entry
Database: EMDB / ID: 8505
TitleStructural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
SampleNon-stop ribosomal complex with ArfA and RF2
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Escherichia coli (strain k12) / bacteria /
Map data
Methodsingle particle reconstruction, at 3.5 Å resolution
AuthorsZeng F / Chen Y
CitationNature, 2017, 541, 554-557

Nature, 2017, 541, 554-557 Yorodumi Papers
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.
Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin

Validation ReportPDB-ID: 5u4i

SummaryFull reportAbout validation report
DateDeposition: Dec 4, 2016 / Header (metadata) release: Jan 4, 2017 / Map release: Jan 11, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5u4i
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8505.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.19 Å/pix.
= 458.112 Å
384 pix
1.19 Å/pix.
= 458.112 Å
384 pix
1.19 Å/pix.
= 458.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.193 Å
Density
Contour Level:0.02 (by author), 0.017 (movie #1):
Minimum - Maximum-0.061812814 - 0.11835373
Average (Standard dev.)7.0680926E-6 (0.0042961156)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 458.112 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1931.1931.193
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z458.112458.112458.112
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0620.1180.000

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Supplemental data

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Sample components

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Entire Non-stop ribosomal complex with ArfA and RF2

EntireName: Non-stop ribosomal complex with ArfA and RF2 / Number of components: 117

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Component #1: protein, Non-stop ribosomal complex with ArfA and RF2

ProteinName: Non-stop ribosomal complex with ArfA and RF2 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, 30S subunit

ProteinName: 30S subunit / Recombinant expression: No

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Component #3: protein, 50S subunit

ProteinName: 50S subunit / Recombinant expression: No

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Component #4: cellular-component, Alternative ribosome-rescue factor A

Cellular-componentName: Alternative ribosome-rescue factor A / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET28 / Strain: BL21

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Component #5: cellular-component, Peptide chain release factor 2

Cellular-componentName: Peptide chain release factor 2 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pETNKI-his3C-LIC-Kan / Strain: BL21

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Component #6: cellular-component, P-site or E-site fMet-tRNA(fMet)

Cellular-componentName: P-site or E-site fMet-tRNA(fMet) / Details: fMet tRNA was in vitro transcribed / Recombinant expression: No

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Component #7: cellular-component, mRNA

Cellular-componentName: mRNA / Recombinant expression: No

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Component #8: cellular-component, 23S rRNA

Cellular-componentName: 23S rRNA / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #9: cellular-component, 50S ribosomal protein L2

Cellular-componentName: 50S ribosomal protein L2 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #10: cellular-component, 16S rRNA

Cellular-componentName: 16S rRNA / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #11: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #12: cellular-component, 30S ribosomal protein S3

Cellular-componentName: 30S ribosomal protein S3 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #13: cellular-component, 30S ribosomal protein S4

Cellular-componentName: 30S ribosomal protein S4 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #14: cellular-component, 30S ribosomal protein S5

Cellular-componentName: 30S ribosomal protein S5 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #15: cellular-component, 30S ribosomal protein S6

Cellular-componentName: 30S ribosomal protein S6 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #16: cellular-component, 30S ribosomal protein S7

Cellular-componentName: 30S ribosomal protein S7 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #17: cellular-component, 30S ribosomal protein S8

Cellular-componentName: 30S ribosomal protein S8 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #18: cellular-component, 30S ribosomal protein S9

Cellular-componentName: 30S ribosomal protein S9 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #19: cellular-component, 30S ribosomal protein S10

Cellular-componentName: 30S ribosomal protein S10 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #20: cellular-component, 30S ribosomal protein S11

Cellular-componentName: 30S ribosomal protein S11 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #21: cellular-component, 30S ribosomal protein S12

Cellular-componentName: 30S ribosomal protein S12 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #22: cellular-component, 30S ribosomal protein S13

Cellular-componentName: 30S ribosomal protein S13 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #23: cellular-component, 30S ribosomal protein S14

Cellular-componentName: 30S ribosomal protein S14 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #24: cellular-component, 30S ribosomal protein S15

Cellular-componentName: 30S ribosomal protein S15 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #25: cellular-component, 30S ribosomal protein S16

Cellular-componentName: 30S ribosomal protein S16 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #26: cellular-component, 30S ribosomal protein S17

Cellular-componentName: 30S ribosomal protein S17 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #27: cellular-component, 30S ribosomal protein S18

Cellular-componentName: 30S ribosomal protein S18 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #28: cellular-component, 30S ribosomal protein S19

Cellular-componentName: 30S ribosomal protein S19 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #29: cellular-component, 30S ribosomal protein S20

Cellular-componentName: 30S ribosomal protein S20 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #30: cellular-component, 30S ribosomal protein S21

Cellular-componentName: 30S ribosomal protein S21 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #31: cellular-component, 50S ribosomal protein L3

Cellular-componentName: 50S ribosomal protein L3 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #32: cellular-component, 50S ribosomal protein L4

Cellular-componentName: 50S ribosomal protein L4 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #33: cellular-component, 50S ribosomal protein L5

Cellular-componentName: 50S ribosomal protein L5 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #34: cellular-component, 50S ribosomal protein L6

Cellular-componentName: 50S ribosomal protein L6 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #35: cellular-component, 50S ribosomal protein L9

Cellular-componentName: 50S ribosomal protein L9 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #36: cellular-component, 50S ribosomal protein L11

Cellular-componentName: 50S ribosomal protein L11 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #37: cellular-component, 50S ribosomal protein L13

Cellular-componentName: 50S ribosomal protein L13 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #38: cellular-component, 50S ribosomal protein L14

Cellular-componentName: 50S ribosomal protein L14 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #39: cellular-component, 50S ribosomal protein L15

Cellular-componentName: 50S ribosomal protein L15 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #40: cellular-component, 50S ribosomal protein L16

Cellular-componentName: 50S ribosomal protein L16 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #41: cellular-component, 50S ribosomal protein L17

Cellular-componentName: 50S ribosomal protein L17 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #42: cellular-component, 50S ribosomal protein L18

Cellular-componentName: 50S ribosomal protein L18 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #43: cellular-component, 50S ribosomal protein L19

Cellular-componentName: 50S ribosomal protein L19 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #44: cellular-component, 50S ribosomal protein L20

Cellular-componentName: 50S ribosomal protein L20 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #45: cellular-component, 50S ribosomal protein L21

Cellular-componentName: 50S ribosomal protein L21 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #46: cellular-component, 50S ribosomal protein L22

Cellular-componentName: 50S ribosomal protein L22 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #47: cellular-component, 50S ribosomal protein L23

Cellular-componentName: 50S ribosomal protein L23 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #48: cellular-component, 50S ribosomal protein L24

Cellular-componentName: 50S ribosomal protein L24 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #49: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #50: cellular-component, 50S ribosomal protein L27

Cellular-componentName: 50S ribosomal protein L27 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #51: cellular-component, 50S ribosomal protein L28

Cellular-componentName: 50S ribosomal protein L28 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #52: cellular-component, 50S ribosomal protein L29

Cellular-componentName: 50S ribosomal protein L29 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #53: cellular-component, 50S ribosomal protein L30

Cellular-componentName: 50S ribosomal protein L30 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #54: cellular-component, 50S ribosomal protein L32

Cellular-componentName: 50S ribosomal protein L32 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #55: cellular-component, 50S ribosomal protein L33

Cellular-componentName: 50S ribosomal protein L33 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #56: cellular-component, 50S ribosomal protein L34

Cellular-componentName: 50S ribosomal protein L34 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #57: cellular-component, 50S ribosomal protein L35

Cellular-componentName: 50S ribosomal protein L35 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #58: cellular-component, 50S ribosomal protein L36

Cellular-componentName: 50S ribosomal protein L36 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #59: cellular-component, 5S rRNA

Cellular-componentName: 5S rRNA / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #60: nucleic-acid, 23S rRNA

Nucleic-acidName: 23S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAU(1MG)(PSU)(5MU)GAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAACCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGG(PSU)GCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG CGAAGGUGUG CUGUGAGGCA UGCUGGAGGU AUCAGAAGUG CGAAUGCUGA CAUAAGUAAC GAUAAAGCGG GUGAAAAGCC CGCUCGCCGG AAGACCAAGG GUUCCUGUCC AACGUUAAUC GGGGCAGGGU GAGUCGACCC CUAAGGCGAG GCCGAAAGGC GUAGUCGAUG GGAAACAGGU UAAUAUUCCU GUACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGCGU GAUGACGAGG CACUACGGUG CUGAAGCAAC AAAUGCCCUG CUUCCAGGAA AAGCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACACAGG 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)AACUA(PSU)AAC GGUCCUAAGG UAGCGAAA(5MU)U CCUUGUCGGG UAAGUUCCGA C(5MC)UGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUGA AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGUGA ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUGGAGC CGACCUUGAA AUACCACCCU UUAAUGUUUG AUGUUCUAAC GUUGACCCGU AAUCCGGGUU GCGGACAGUG UCUGGUGGGU AGUUUGACUG (OMG)GGCGGUCUC CUCCUAAAGA GUAACGGAGG AGCACGAAGG UUGGCUAAUC CUGGUCGGAC AUCAGGAGGU UAGUGCAAUG GCAUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCG(2MG)GGAUA ACAGGC(PSU)GAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCA(OMC)CU CGA(PSU)GUCGGC UCAUCACAUC CUGGGGCUGA AGUAGGUCCC AAGGGUAUGG C(OMU)GUUCGCCA UUUAAAGUGG UACGCGAGC(PSU) GGGUUUAGAA CGUCGUGAGA CAGU(PSU)CGGUC CCUAUCUGCC GUGGGCGCUG GAGAACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACUGCCCGGU AGCUAAAUGC GGAAGAGAUA AGUGCUGAAA GCAUCUAAGC ACGAAACUUG CCCCGAGAUG AGUUCUCCCU GACCCUUUAA GGGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCUU
MassTheoretical: 941.761625 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #61: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCUGGCGGC CGUAGCGCGG UGGUCCCACC UGACCCCAUG CCGAACUCAG AAGUGAAACG CCGUAGCGCC GAUGGUAGUG UGGGGUCUCC CCAUGCGAGA GUAGGGAACU GCCAGGCA
MassTheoretical: 38.177762 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #62: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Details: Gene Name(s): rplB b3317 JW3279 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #63: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Details: Gene Name(s): rplC b3320 JW3282 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #64: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Details: Gene Name(s): rplD eryA b3319 JW3281 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #65: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Details: Gene Name(s): rplE b3308 JW3270 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #66: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Details: Gene Name(s): rplF b3305 JW3267 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #67: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Details: Gene Name(s): rplI b4203 JW4161 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #68: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Details: Gene Name(s): rplK relC b3983 JW3946 / Recombinant expression: No
MassTheoretical: 14.894362 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #69: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Details: Gene Name(s): rplM b3231 JW3200 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #70: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Details: Gene Name(s): rplN b3310 JW3272 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #71: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Details: Gene Name(s): rplO b3301 JW3263 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #72: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Details: Gene Name(s): rplP b3313 JW3275 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

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Component #73: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Details: Gene Name(s): rplQ b3294 JW3256 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #74: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Details: Gene Name(s): rplR b3304 JW3266 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #75: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Details: Gene Name(s): rplS b2606 JW2587 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #76: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Details: Gene Name(s): rplT pdzA b1716 JW1706 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #77: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Details: Gene Name(s): rplU b3186 JW3153 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #78: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Details: Gene Name(s): rplV eryB b3315 JW3277 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #79: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Details: Gene Name(s): rplW b3318 JW3280 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #80: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Details: Gene Name(s): rplX b3309 JW3271 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #81: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Details: Gene Name(s): rplY b2185 JW2173 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #82: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Details: Gene Name(s): rpmA b3185 JW3152 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #83: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Details: Gene Name(s): rpmB b3637 JW3612 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #84: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Details: Gene Name(s): rpmC b3312 JW3274 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #85: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Details: Gene Name(s): rpmD b3302 JW3264 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #86: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Details: Gene Name(s): rpmF b1089 JW1075 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #87: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Details: Gene Name(s): rpmG b3636 JW3611 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #88: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Details: Gene Name(s): rpmH rimA ssaF b3703 JW3680 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #89: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Details: Gene Name(s): rpmI b1717 JW1707 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #90: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Details: Gene Name(s): rpmJ b3299 JW3261 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #91: 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 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 UCCG(PSU)GCCAG CAGCCACGGU 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 CGAU(2MG)(5MC)AACG CGAAGAACCU UACCUGGUCU UGACAUCCAC GGAAGUUUUC AGAGAUGAGA AUGUGCCUUC GGGAACCGUG AGACAGGUGC UGCAUGGCUG UCGUCAGCUC GUGUUGUGAA AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUUAUCCU UUGUUGCCAG CGGUCCGGCC GGGAACUCAA AGGAGACUGC CAGUGAUAAA CUGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUG(2MG)CCCU UACGACCAGG GCUACACACG UGCUACAAUG GCGCAUACAA AGAGAAGCGA CCUCGCGAGA GCAAGCGGAC CUCAUAAAGU GCGUCGUAGU CCGGAUUGGA GUCUGCAACU CGACUCCAUG AAGUCGGAAU CGCUAGUAAU CGUGGAUCAG AAUGCCACGG UGAAUACGUU CCCGGGCCUU GUACACACCG (4OC)CCGU(5MC)ACAC CAUGGGAGUG GGUUGCAAAA GAAGUAGGUA GCUUAACCUU CGGGAGGGCG CUUACCACUU UGUGAUUCAU GACUGGGGUG AAGUCG(UR3)AAC AAGGUAACCG UAGG(2MG)G(MA6)(MA6)CC UGCGGUUGGA UCA
MassTheoretical: 497.04475 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

+
Component #92: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Details: Gene Name(s): rpsB b0169 JW0164 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #93: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Details: Gene Name(s): rpsC b3314 JW3276 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #94: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Details: Gene Name(s): rpsD ramA b3296 JW3258 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #95: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Details: Gene Name(s): rpsE spc b3303 JW3265 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #96: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Details: Gene Name(s): rpsF b4200 JW4158 / Recombinant expression: No
MassTheoretical: 15.727512 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #97: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Details: Gene Name(s): rpsG b3341 JW3303 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria / / Strain: K12

+
Component #98: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Details: Gene Name(s): rpsH b3306 JW3268 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #99: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Details: Gene Name(s): rpsI b3230 JW3199 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #100: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Details: Gene Name(s): rpsJ nusE b3321 JW3283 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #101: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Details: Gene Name(s): rpsK b3297 JW3259 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #102: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Details: Gene Name(s): rpsL strA b3342 JW3304 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #103: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Details: Gene Name(s): rpsM b3298 JW3260 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #104: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Details: Gene Name(s): rpsN b3307 JW3269 / Recombinant expression: No
MassTheoretical: 11.475364 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #105: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Details: Gene Name(s): rpsO secC b3165 JW3134 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #106: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Details: Gene Name(s): rpsP b2609 JW2590 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #107: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Details: Gene Name(s): rpsQ neaA b3311 JW3273 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #108: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Details: Gene Name(s): rpsR b4202 JW4160 / Recombinant expression: No
MassTheoretical: 9.063508 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #109: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Details: Gene Name(s): rpsS b3316 JW3278 / Recombinant expression: No
MassTheoretical: 9.349939 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #110: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Details: Gene Name(s): rpsT b0023 JW0022 / Recombinant expression: No
MassTheoretical: 9.577268 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #111: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Details: Gene Name(s): rpsU b3065 JW3037 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

+
Component #112: protein, Peptide chain release factor 2

ProteinName: Peptide chain release factor 2 / Details: Gene Name(s): prfB ECK2886 JW5847 supK / Recombinant expression: No
MassTheoretical: 43.313871 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

+
Component #113: protein, Alternative ribosome-rescue factor A

ProteinName: Alternative ribosome-rescue factor A / Recombinant expression: No
MassTheoretical: 6.513396 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

+
Component #114: nucleic-acid, P-site or E-site fMet-tRNA(fMet)

Nucleic-acidName: P-site or E-site fMet-tRNA(fMet) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGGUUCAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.802785 kDa

+
Component #115: nucleic-acid, mRNA

Nucleic-acidName: mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCAAGGAGG UAAAAAUG
MassTheoretical: 5.922644 kDa

+
Component #116: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 124 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #117: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 83822 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 155440
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

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External links: The 2017 Nobel Prize in Chemistry - Press Release

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