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- EMDB-10655: E. coli 50S ribosomal subunit in complex with dirithromycin, fMet... -

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Basic information

Entry
Database: EMDB / ID: EMD-10655
TitleE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).
Map data
SampleE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).:
E. coli 50S ribosomal subunit / fMet-Phe-tRNA(Phe) / (nucleic-acidNucleic acid) x 4 / (50S ribosomal protein ...) x 29 / (ligand) x 3
Function / homology
Function and homology information


stringent response / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / ribosome assembly ...stringent response / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / ribosome assembly / DNA-templated transcription, termination / response to reactive oxygen species / translational termination / regulation of cell growth / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / ribosome biogenesis / response to radiation / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / cytosol
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L10 ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, N-terminal / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L11, C-terminal / Ribosomal protein L33, conserved site / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L33 signature. / Ribosomal protein L11, RNA binding domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal L28 family / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / Ribosomal protein L20 / L28p-like / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal L32p protein family / Ribosomal L27 protein / Ribosomal protein L27 / Ribosomal protein L21 / Ribosomal protein L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L17 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L13, bacterial-type / Ribosomal protein L24 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature.
Similarity search - Domain/homology
50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L16 / 50S ribosomal protein L4 ...50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L16 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L23 / 50S ribosomal protein L35 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / 50S ribosomal protein L36 / 50S ribosomal protein L34 / 50S ribosomal protein L33 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 50S ribosomal protein L28 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L19 / 50S ribosomal protein L11 / 50S ribosomal protein L10 / 50S ribosomal protein L15 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Saccharomyces cerevisiae (baker's yeast) / baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsPichkur EB / Polikanov YS / Myasnikov AG / Konevega AL
Funding support Russian Federation, United States, 5 items
OrganizationGrant numberCountry
Russian Science Foundation17-14-01416 Russian Federation
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI137584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM132302 United States
Russian Science Foundation18-44-04005 Russian Federation
Russian Foundation for Basic Research17-00-00366 Russian Federation
CitationJournal: RNA / Year: 2020
Title: Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the 70S ribosome.
Authors: Evgeny B Pichkur / Alena Paleskava / Andrey G Tereshchenkov / Pavel Kasatsky / Ekaterina S Komarova / Dmitrii I Shiriaev / Alexey A Bogdanov / Olga A Dontsova / Ilya A Osterman / Petr V ...Authors: Evgeny B Pichkur / Alena Paleskava / Andrey G Tereshchenkov / Pavel Kasatsky / Ekaterina S Komarova / Dmitrii I Shiriaev / Alexey A Bogdanov / Olga A Dontsova / Ilya A Osterman / Petr V Sergiev / Yury S Polikanov / Alexander G Myasnikov / Andrey L Konevega /
Abstract: Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and ...Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
History
DepositionFeb 3, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xz7
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10655.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å
0.86 Å/pix.
x 512 pix.
= 440.32 Å
0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-1.2119176 - 2.7087216
Average (Standard dev.)0.00017308077 (±0.036652006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z440.320440.320440.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2122.7090.000

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Supplemental data

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Segmentation: #1

Fileemd_10655_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: A map calculated and sharpened in CisTEM before...

Fileemd_10655_additional.map
AnnotationA map calculated and sharpened in CisTEM before high-order aberrations correction in Relion 3.1.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: Half #2

Fileemd_10655_half_map_1.map
AnnotationHalf #2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: Half #1

Fileemd_10655_half_map_2.map
AnnotationHalf #1
Projections & Slices
AxesZYX

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Sample components

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Entire E. coli 50S ribosomal subunit in complex with dirithromycin, fMet...

EntireName: E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).
Number of components: 39

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Component #1: protein, E. coli 50S ribosomal subunit in complex with dirithromy...

ProteinName: E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).
Recombinant expression: No
MassTheoretical: 2.7 MDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #2: protein, E. coli 50S ribosomal subunit

ProteinName: E. coli 50S ribosomal subunit / Recombinant expression: No
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #3: protein, fMet-Phe-tRNA(Phe)

ProteinName: fMet-Phe-tRNA(Phe) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU ...Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAU(1MG)(PSU)(5MU)GAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCACUUA CCAACCCGAU GCAAACUGCG AAUACCGGAG AAUGUUAUCA CGGGAGACAC ACGGCGGG(PSU)G CUAACGUCCG UCGUGAAGAG GGAAACAACC CAGACCGCCA GCUAAGGUCC CAAAGUCAUG GUUAAGUGGG AAACGAUGUG GGAAGGCCCA GACAGCCAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAAAGCGUAA UAGCUCACUG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUCUGUAAG CCUGCGAAGG UGUGCUGUGA GGCAUGCUGG AGGUAUCAGA AGUGCGAAUG CUGACAUAAG UAACGAUAAA GCGGGUGAAA AGCCCGCUCG CCGGAAGACC AAGGGUUCCU GUCCAACGUU AAUCGGGGCA GGGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGAAGG CUAUGUUGGC CGGGCGACGG UUGUCCCGGU UUAAGCGUGU AGGCUGGUUU UCCAGGCAAA UCCGGAAAAU CAAGGCUGAG GCGUGAUGAC GAGGCACUAC GGUGCUGAAG CAACAAAUGC CCUGCUUCCA GGAAAAGCCU CUAAGCAUCA GGUAACAUCA AAUCGUACCC CAAACCGACA C(6MZ)GGUGGUCA GGUAGAGAAU ACCAAGGCGC UUGAGAGAAC UCGGGUGAAG GAACUAGGCA AAAUGGUGCC GUAACUUCGG GAGAAGGCAC GCUGAUAUGU AGGUGAGGUC CCUCGCGGAU GGAGCUGAAA UCAGUCGAAG AUACCAGCUG GCUGCAACUG UUUAUUAAAA ACACAGCACU GUGCAAACAC GAAAGUGGAC GUAUACGGUG UGACGCCU(2MG)C CCGGUGCCGG AAGGUUAAUU GAUGGGGUUA GCGCAAGCGA AGCUCUUGAU CGAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGAC(5MC)UGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGAC UCAGUGAAAU UGAACUCGCU GUG(6MZ)AGAUGC AGUGUACCCG CGGCAAGACG GAAAGACCCC GU(G7M)AACCUUU ACUAUAGCUU GACACUGAAC AUUGAGCCUU GAUGUGUAGG AUAGGUGGGA GGCUUUGAAG UGUGGACGCC AGUCUGCAUG GAGCCGACCU UGAAAUACCA CCCUUUAAUG UUUGAUGUUC UAACGUUGAC CCGUAAUCCG GGUUGCGGAC AGUGUCUGGU GGGUAGUUUG ACUG(OMG)GGCGG UCUCCUCCUA AAGAGUAACG GAGGAGCACG AAGGUUGGCU AAUCCUGGUC GGACAUCAGG AGGUUAGUGC AAUGGCAUAA GCCAGCUUGA CUGCGAGCGU GACGGCGCGA GCAGGUGCGA AAGCAGGUCA UAGUGAUCCG GUGGUUCUGA AUGGAAGGGC CAUCGCUCAA CGGAUAAAAG GUACUCCG(2MG)G GA(H2U)AACAGGC (PSU)GAUACCGCC CAAGAGUUCA UAUCGACGGC GGUGUUUGGC A(OMC)CUCG(2MA)(PSU)GU CGGCUCAUCA CAUCCUGGGG CUGAAGUAGG UCCCAAGGGU AUGGC(OMU)GUUC GCCAUUUAAA GUGGUACGCG AGC(PSU)GGGUUU AGAACGUCGU GAGACAG(PSU)(PSU)C GGUCCCUAUC UGCCGUGGGC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACUGCC CGGUAGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAAGGGUCC UGAAGGAACG UUGAAGACGA CGACGUUGAU AGGCCGGGUG UGUAAGCGCA GCGAUGCGUU GAGCUAACCG GUACUAAUGA ACCGUGAGGC UUAACCU
MassTheoretical: 939.60925 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #5: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S 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 (strain K12) (bacteria)

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Component #6: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #7: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.291562 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #8: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #9: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #10: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #11: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.568748 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #12: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.020303 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #13: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #14: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #15: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #16: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.327261 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #17: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.193465 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #18: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #19: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #20: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #21: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #22: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #23: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #24: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.078874 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #25: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #26: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.275498 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #27: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #28: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.155267 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #29: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #30: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #31: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.928 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #32: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #33: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #34: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #35: nucleic-acid, Deacylated tRNAi(Met)

nucleic acidName: Deacylated tRNAi(Met) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGGGG(4SU)GGA GCAGCCUGGU AGCUCGUCGG G(5MC)UCAUAACC CGAAGGUCGU CGG(5MU)(PSU)CAAAU CCGGCCCCCG CAACCA
MassTheoretical: 24.541719 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #36: nucleic-acid, fMet-Phe-tRNA(Phe)

nucleic acidName: fMet-Phe-tRNA(Phe) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGGAUUUA(2MG) CUCAG(H2U)(H2U)GGG AGAGC(M2G)CCAG A(OMC)U(OMG)AA(YYG)A(PSU)(5MC) UGGAG(7MG)UC(5MC)U GUG(5MU)(PSU)CG(1MA)UC CACAGAAUUC GCACC(31M)
MassTheoretical: 25.167506 kDa
SourceSpecies: baker's yeast (baker's yeast)

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Component #37: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 178 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #38: ligand, Dirithromycin

LigandName: Dirithromycin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.835074 kDa

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Component #39: ligand, water

LigandName: water / Number of Copies: 528 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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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: 80 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 75000 X (nominal) / Cs: 0.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 300.0 - 2200.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 401905
3D reconstructionSoftware: RELION / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4YBB
Output model

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