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- EMDB-21856: 50S ribosomal subunit without free 5S rRNA and perturbed PTC -

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Basic information

Entry
Database: EMDB / ID: EMD-21856
Title50S ribosomal subunit without free 5S rRNA and perturbed PTC
Map dataCryo-EM map of inactive 50S ribosomal subunit with 23s-cp5s
Sample
  • Complex: 50S ribosomal subunit without free 5S rRNA and perturbed PTC
    • Protein or peptide: x 30 types
    • RNA: x 1 types
KeywordsRibosome / 23S-cp5S rRNA / engineering
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation ...negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form ...Ribosomal protein L1, bacterial-type / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLoveland AB / Korostelev AA
Funding support United States, Estonia, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127134 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
Estonian Research CouncilPUT669 Estonia
National Aeronautic Space Administration (NASA, United States)80NSSC17K0031 United States
CitationJournal: Nat Commun / Year: 2020
Title: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
Authors: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin /
Abstract: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis.
History
DepositionApr 23, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wnt
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21856.png

Downloads & links

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Map

FileDownload / File: emd_21856.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of inactive 50S ribosomal subunit with 23s-cp5s
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-6.456271 - 19.137633999999998
Average (Standard dev.)0.0007873699 (±0.77386004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions608608608
Spacing608608608
CellA=B=C: 528.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z608608608
origin x/y/z0.0000.0000.000
length x/y/z528.960528.960528.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS608608608
D min/max/mean-6.45619.1380.001

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Supplemental data

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Half map: Cryo-EM half map of inactive 50S ribosomal subunit with 23s-cp5s

Fileemd_21856_half_map_1.map
AnnotationCryo-EM half map of inactive 50S ribosomal subunit with 23s-cp5s
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 2 of inactive 50S ribosomal subunit with 23s-cp5s

Fileemd_21856_half_map_2.map
AnnotationCryo-EM half map 2 of inactive 50S ribosomal subunit with 23s-cp5s
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 50S ribosomal subunit without free 5S rRNA and perturbed PTC

EntireName: 50S ribosomal subunit without free 5S rRNA and perturbed PTC
Components
  • Complex: 50S ribosomal subunit without free 5S rRNA and perturbed PTC
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L10
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein L1
    • RNA: 23s-5s joint ribosomal RNA

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Supramolecule #1: 50S ribosomal subunit without free 5S rRNA and perturbed PTC

SupramoleculeName: 50S ribosomal subunit without free 5S rRNA and perturbed PTC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 29.663244 KDa
SequenceString: AVVKCKPTSP GRRHVVKVVN PELHKGKPFA PLLEKNSKSG GRNNNGRITT RHIGGGHKQA YRIVDFKRNK DGIPAVVERL EYDPNRSAN IALVLYKDGE RRYILAPKGL KAGDQIQSGV DAAIKPGNTL PMRNIPVGST VHNVEMKPGK GGQLARSAGT Y VQIVARDG ...String:
AVVKCKPTSP GRRHVVKVVN PELHKGKPFA PLLEKNSKSG GRNNNGRITT RHIGGGHKQA YRIVDFKRNK DGIPAVVERL EYDPNRSAN IALVLYKDGE RRYILAPKGL KAGDQIQSGV DAAIKPGNTL PMRNIPVGST VHNVEMKPGK GGQLARSAGT Y VQIVARDG AYVTLRLRSG EMRKVEADCR ATLGEVGNAE HMLRVLGKAG AARWRGVRPT VRGTAMNPVD HPHGGGEGRN FG KHPVTPW GVQTKGKKTR SNKRTDKFIV RRRS

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #2: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 22.277535 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #3: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 22.121566 KDa
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #4: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 20.073234 KDa
SequenceString:
AKLHDYYKDE VVKKLMTEFN YNSVMQVPRV EKITLNMGVG EAIADKKLLD NAAADLAAIS GQKPLITKAR KSVAGFKIRQ GYPIGCKVT LRGERMWEFF ERLITIAVPR IRDFRGLSAK SFDGRGNYSM GVREQIIFPE IDYDKVDRVR GLDITITTTA K SDEEGRAL LAAFDFPFR

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #5: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 18.801598 KDa
SequenceString:
SRVAKAPVVV PAGVDVKING QVITIKGKNG ELTRTLNDAV EVKHADNTLT FGPRDGYADG WAQAGTARAL LNSMVIGVTE GFTKKLQLV GVGYRAAVKG NVINLSLGFS HPVDHQLPAG ITAECPTQTE IVLKGADKQV IGQVAADLRA YRRPEPYKGK G VRYADEVV RTKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #6: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #7: 50S ribosomal protein L10

MacromoleculeName: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 14.112345 KDa
SequenceString:
MALNLQDKQA IVAEVSEVAK GALSAVVADS RGVTVDKMTE LRKAGREAGV YMRVVRNTLL RRAVEGTPFE CLKDAFVGPT LIAYSMEHP GAAARLFKEF AKANAKFEVK AAAFEGELIP ASQIDRLATL PT

UniProtKB: Large ribosomal subunit protein uL10

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Macromolecule #8: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 14.763165 KDa
SequenceString:
AKKVQAYVKL QVAAGMANPS PPVGPALGQQ GVNIMEFCKA FNAKTDSIEK GLPIPVVITV YADRSFTFVT KTPPAAVLLK KAAGIKSGS GKPNKDKVGK ISRAQLQEIA QTKAADMTGA DIEAMTRSIE GTARSMGLVV ED

UniProtKB: Large ribosomal subunit protein uL11

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Macromolecule #9: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #10: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.45191 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEV

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #11: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 14.877273 KDa
SequenceString:
RLNTLSPAEG SKKAGKRLGR GIGSGLGKTG GRGHKGQKSR SGGGVRRGFE GGQMPLYRRL PKFGFTSRKA AITAEIRLSD LAKVEGGVV DLNTLKAANI IGIQIEFAKV ILAGEVTTPV TVRGLRVTKG ARAAIEAAGG KIEE

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #12: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.721938 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS E

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #13: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 12.663471 KDa
SequenceString:
DKKSARIRRA TRARRKLQEL GATRLVVHRT PRHIYAQVIA PNGSEVLVAA STVEKAIAEQ LKYTGNKDAA AAVGKAVAER ALEKGIKDV SFDRSGFQYH GRVQALADAA REAGLQF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #14: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.028082 KDa
SequenceString:
SNIIKQLEQE QMKQDVPSFR PGDTVEVKVW VVEGSKKRLQ AFEGVVIAIR NRGLHSAFTV RKISNGEGVE RVFQTHSPVV DSISVKRRG AVRKAKLYYL RERTGKAARI KERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #15: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.396828 KDa
SequenceString:
ARVKRGVIAR ARHKKILKQA KGYYGARSRV YRVAFQAVIK AGQYAYRDRR QRKRQFRQLW IARINAAARQ NGISYSKFIN GLKKASVEI DRKILADIAV FDKVAFTALV EKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #16: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #17: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #18: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 10.546472 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNL

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #19: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 11.078874 KDa
SequenceString:
AAKIRRDDEV IVLTGKDKGK RGKVKNVLSS GKVIVEGINL VKKHQKPVPA LNQPGGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDG KKVRFFKSNS ETI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #20: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #21: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 8.174394 KDa
SequenceString:
RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #22: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 8.896354 KDa
SequenceString:
SRVCQVTGKR PVTGNNRSHA LNATKRRFLP NLHSHRFWVE SEKRFVTLRV SAKGMRVIDK KGIDTVLAEL RARGEKY

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #23: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #24: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 6.423625 KDa
SequenceString:
AKTIKITQTR SAIGRLPKHK ATLLGLGLRR IGHTVEREDT PAIRGMINAV SFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #25: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 7.887117 KDa
SequenceString:
MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNIPGSK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #26: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 6.332249 KDa
SequenceString:
AVQQNKPTRS KRGMRRSHDA LTAVTSLSVD KTSGEKHLRH HITADGYYRG RKVIAK

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #27: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #28: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 7.181835 KDa
SequenceString:
PKIKTVRGAA KRFKKTGKGG FKHKHANLRH ILTKKATKRK RHLRPKAMVS KGDLGLVIAC LPYA

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #29: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 4.37739 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36A

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Macromolecule #30: 50S ribosomal protein L1

MacromoleculeName: 50S ribosomal protein L1 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 23.735498 KDa
SequenceString: KLTKRMRVIR EKVDATKQYD INEAIALLKE LATAKFVESV DVAVNLGIDA RKSDQNVRGA TVLPHGTGRS VRVAVFTQGA NAEAAKAAG AELVGMEDLA DQIKKGEMNF DVVIASPDAM RVVGQLGQVL GPRGLMPNPK VGTVTPNVAE AVKNAKAGQV R YRNDKNGI ...String:
KLTKRMRVIR EKVDATKQYD INEAIALLKE LATAKFVESV DVAVNLGIDA RKSDQNVRGA TVLPHGTGRS VRVAVFTQGA NAEAAKAAG AELVGMEDLA DQIKKGEMNF DVVIASPDAM RVVGQLGQVL GPRGLMPNPK VGTVTPNVAE AVKNAKAGQV R YRNDKNGI IHTTIGKVDF DADKLKENLE ALLVALKKAK PTQAKGVYIK KVSISTTMGA GVAVD

UniProtKB: Large ribosomal subunit protein uL1

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Macromolecule #31: 23s-5s joint ribosomal RNA

MacromoleculeName: 23s-5s joint ribosomal RNA / type: rna / ID: 31
Details: Engineered 23S rRNA with inserted circularly permuted 5S rRNA
Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 982.729812 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAUGUCGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUGCUA A CGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGCU GCUCCCCAUG CG AGAGUAG GGAACUGCCA GGCAUUCGGU GCCUGGCGGC CGUAGCGCGG UGGUCCCACC UGACCCCAUG CCGAACUCAG AAG UGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUAAA ACGAUGUGGG AAGGCCCAGA CAGCCAGGAU GUUGGCUUAG AAGC AGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGGC CUGCGCGGAA GAUGUAACGG GGCUAAACCA UGCAC CGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUCUGUAAG CCUGCGAAGG UGUGCUGUGA GGCAUG CUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA AGCGGGUGAA AAGCCCGCUC GCCGGAAGAC CAAGGGU UC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAGGCCG AAAGGCGUAG UCGAUGGGAA ACAGGUUA A UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGGCUAUGUU GGCCGGGCGA CGGUUGUCCC GGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAGGCGUGA UGACGAGGCA CUACGGUGCU GAAGCAACAA AUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCAAAUCG UACCCCAAAC CGACACAGGU GGUCAGGUAG A GAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUAA CUUCGGGAGA AGGCACGCUG AU AUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGAAAUCA GUCGAAGAUA CCAGCUGGCU GCAACUGUUU AUUAAAAACA CAG CACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGCCC GGUGCCGGAA GGUUAAUUGA UGGGGUUAGC GCAA GCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUAU AACGGUCCUA AGGUAGCGAA AUUCCUUGUC GGGUA AGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGAC UCAGUGAAAU UGAACUCGCU GUGAAG AUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUGAACCUU UACUAUAGCU UGACACUGAA CAUUGAGCCU UGAUGUG UA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UGGAGCCGAC CUUGAAAUAC CACCCUUUAA UGUUUGAU G UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGUGGGUAGU UUGACUGGGG CGGUCUCCUC CUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGGAGGUUA GUGCAAUGGC AUAAGCCAGC UUGACUGCGA GCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCGGUGGU UCUGAAUGGA AGGGCCAUCG CUCAACGGAU A AAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCACCU CGAUGUCGGC UC AUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUAUG GCUGUUCGCC AUUUAAAGUG GUACGCGAGC UGGGUUUAGA ACG UCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AGGGGGGCUG CUCCUAGUAC GAGAGGACCG GAGU GGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU GGCACUGCCC GGUAGCUAAA UGCGGAAGAG AUAAGUGCUG AAAGC AUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAAGGGUCC UGAAGGAACG UUGAAGACGA CGACGU UGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGAGCUAACC GGUACUAAUG AACCGUGAGG CUUAACCU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration.1 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2

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Image processing

Particle selectionNumber selected: 489732
Startup modelType of model: EMDB MAP
Initial angle assignmentType: ANGULAR RECONSTITUTION
Software: (Name: cisTEM (ver. 1.0.0-beta), FREALIGN (ver. 9.11))
Final angle assignmentType: ANGULAR RECONSTITUTION
Software: (Name: cisTEM (ver. 1.0.0-beta), FREALIGN (ver. 9.11))
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 21705
FSC plot (resolution estimation)

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