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- EMDB-21562: MultiBody Refinement of 70S Ribosome from Enterococcus faecalis -

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Basic information

Entry
Database: EMDB / ID: EMD-21562
TitleMultiBody Refinement of 70S Ribosome from Enterococcus faecalis
Map data
Sample70S ribosomeRibosome:
(nucleic-acidNucleic acid) x 3 / (30S ribosomal protein ...) x 18 / (50S ribosomal protein ...) x 26 / ligand
Function / homology
Function and homology information


large ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding
Ribosomal protein L3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type ...Ribosomal protein L3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S10, conserved site / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L17 superfamily / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / L28p-like / Ribosomal protein L5, C-terminal / Ribosomal protein L34, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S14, type Z / Ribosomal protein L15 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S3, C-terminal / Ribosomal protein L6 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L15, conserved site / Ribosomal protein S14 / Ribosomal protein L28 / Ribosomal protein L3 / Ribosomal protein S18 / Ribosomal protein L27 / Ribosomal protein L33 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L21 / Ribosomal protein S10 / Ribosomal protein L29/L35 / Ribosomal protein S8
50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L24 / 50S ribosomal protein L17 / 50S ribosomal protein L30 / 30S ribosomal protein S5 / 50S ribosomal protein L32 / 50S ribosomal protein L21 / 50S ribosomal protein L33 ...50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L24 / 50S ribosomal protein L17 / 50S ribosomal protein L30 / 30S ribosomal protein S5 / 50S ribosomal protein L32 / 50S ribosomal protein L21 / 50S ribosomal protein L33 / 30S ribosomal protein S16 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 50S ribosomal protein L29 / 30S ribosomal protein S4 / 30S ribosomal protein S15 / 50S ribosomal protein L28 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L34 / 30S ribosomal protein S11 / 30S ribosomal protein S13 / 50S ribosomal protein L4 / 30S ribosomal protein S3 / 30S ribosomal protein S18 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S12 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 50S ribosomal protein L14 / 50S ribosomal protein L6 / 50S ribosomal protein L5 / 30S ribosomal protein S17 / 30S ribosomal protein S8 / 50S ribosomal protein L18 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L15 / 50S ribosomal protein L22 / 50S ribosomal protein L36 / 50S ribosomal protein L16 / un:a0a449dxs1:
Biological speciesEnterococcus faecalis OG1RF (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJogl G / Khayat R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)G12MD007603 United States
CitationJournal: Sci Rep / Year: 2020
Title: Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
Authors: Eileen L Murphy / Kavindra V Singh / Bryant Avila / Torsten Kleffmann / Steven T Gregory / Barbara E Murray / Kurt L Krause / Reza Khayat / Gerwald Jogl /
Abstract: Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ...Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
Validation ReportPDB-ID: 6w6p

SummaryFull reportAbout validation report
History
DepositionMar 17, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6w6p
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21562.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 440 pix.
= 482.68 Å
1.1 Å/pix.
x 440 pix.
= 482.68 Å
1.1 Å/pix.
x 440 pix.
= 482.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.097 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.019343046 - 0.2261516
Average (Standard dev.)0.0034019458 (±0.0071898615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 482.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0971.0971.097
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z482.680482.680482.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0190.2260.003

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Supplemental data

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Additional map: 50S subunit of 70S Ribosome Enterococcus faecalis MultiBody...

Fileemd_21562_additional_1.map
Annotation50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 30S subunit (body) of 70S Ribosome Enterococcus faecalis...

Fileemd_21562_additional_2.map
Annotation30S subunit (body) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 30S subunit (head) of 70S Ribosome Enterococcus faecalis...

Fileemd_21562_additional_3.map
Annotation30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 70S ribosome

EntireName: 70S ribosomeRibosome / Number of components: 49

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Component #1: protein, 70S ribosome

ProteinName: 70S ribosomeRibosome / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #2: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA ACGCUUCUUU CCUCCCGAGU GCUUGCACUC AAUUGGAAAG AGGAGUGGCG GACGGGUGAG UAACACGUGG GUAACCUACC CAUCAGAGGG GGAUAACACU UGGAAACAGG ...Sequence:
UGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA ACGCUUCUUU CCUCCCGAGU GCUUGCACUC AAUUGGAAAG AGGAGUGGCG GACGGGUGAG UAACACGUGG GUAACCUACC CAUCAGAGGG GGAUAACACU UGGAAACAGG UGCUAAUACC GCAUAACAGU UUAUGCCGCA UGGCAUAAGA GUGAAAGGCG CUUUCGGGUG UCGCUGAUGG AUGGACCCGC GGUGCAUUAG CUAGUUGGUG AGGUAACGGC UCACCAAGGC CACGAUGCAU AGCCGACCUG AGAGGGUGAU CGGCCACACU GGGACUGAGA CACGGCCCAG ACUCCUACGG GAGGCAGCAG UAGGGAAUCU UCGGCAAUGG ACGAAAGUCU GACCGAGCAA CGCCGCGUGA GUGAAGAAGG UUUUCGGAUC GUAAAACUCU GUUGUUAGAG AAGAACAAGG ACGUUAGUAA CUGAACGUCC CCUGACGGUA UCUAACCAGA AAGCCACGGC UAACUACGUG CCAGCAGCCG CGGUAAUACG UAGGUGGCAA GCGUUGUCCG GAUUUAUUGG GCGUAAAGCG AGCGCAGGCG GUUUCUUAAG UCUGAUGUGA AAGCCCCCGG CUCAACCGGG GAGGGUCAUU GGAAACUGGG AGACUUGAGU GCAGAAGAGG AGAGUGGAAU UCCAUGUGUA GCGGUGAAAU GCGUAGAUAU AUGGAGGAAC ACCAGUGGCG AAGGCGGCUC UCUGGUCUGU AACUGACGCU GAGGCUCGAA AGCGUGGGGA GCAAACAGGA UUAGAUACCC UGGUAGUCCA CGCCGUAAAC GAUGAGUGCU AAGUGUUGGA GGGUUUCCGC CCUUCAGUGC UGCAGCAAAC GCAUUAAGCA CUCCGCCUGG GGAGUACGAC CGCAAGGUUG AAACUCAAAG GAAUUGACGG GGGCCCGCAC AAGCGGUGGA GCAUGUGGUU UAAUUCGAAG CAACGCGAAG AACCUUACCA GGUCUUGACA UCCUUUGACC ACUCUAGAGA UAGAGCUUUC CCUUCGGGGA CAAAGUGACA GGUGGUGCAU GGUUGUCGUC AGCUCGUGUC GUGAGAUGUU GGGUUAAGUC CCGCAACGAG CGCAACCCUU AUUGUUAGUU GCCAUCAUUU AGUUGGGCAC UCUAGCGAGA CUGCCGGUGA CAAACCGGAG GAAGGUGGGG AUGACGUCAA AUCAUCAUGC CCCUUAUGAC CUGGGCUACA CACGUGCUAC AAUGGGAAGU ACAACGAGUC GCUAGACCGC GAGGUCAUGC AAAUCUCUUA AAGCUUCUCU CAGUUCGGAU UGCAGGCUGC AACUCGCCUG CAUGAAGCCG GAAUCGCUAG UAAUCGCGGA UCAGCACGCC GCGGUGAAUA CGUUCCCGGG CCUUGUACAC ACCGCCCGUC ACACCACGAG AGUUUGUAAC ACCCGAAGUC GGUGAGGUAA CCUUUUUGGA GCCAGCCGCC UAAGGUGGGA UAGAUGAUUG GGGUGAAGUC GUAACAAGGU AGCCGUAUCG GAAGGUGCGG CUGGAUCA
MassTheoretical: 501.090781 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.884309 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.029299 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.156979 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #6: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.331838 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #7: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.547219 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #8: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.805198 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #9: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.069206 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #10: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.400286 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #11: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.3221 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #12: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.178622 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #13: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.619492 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #14: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.041397 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #15: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.537042 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #16: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.095773 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #17: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.74437 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #18: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.646979 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #19: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.999471 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #20: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.841125 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #21: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAAG UAAGCUAUGA UCCAGAGAUU UCCGAAUGGG GGAACCCAAU AUCUUUUAUA GGAUAUUACU UUUCAGUGAA UACAUAGCUG ...Sequence:
UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAAG UAAGCUAUGA UCCAGAGAUU UCCGAAUGGG GGAACCCAAU AUCUUUUAUA GGAUAUUACU UUUCAGUGAA UACAUAGCUG AUUAGAGGUA GACGCAGAGA ACUGAAACAU CUUAGUACCU GCAGGAAGAG AAAGAAAAUU CGAUUCCCUG AGUAGCGGCG AGCGAAACGG GAAGAGCCCA AACCAACAAG CUUGCUUGUU GGGGUUGUAG GACUCCGAUA UGGUAGUCUG UUAGUAUAGU UGAAGGAUUU GGAAAAUUCC GCUAAAGAGG GUGAAAGCCC CGUAGACGAA AUGCUGACAA CACCUAGGAG GAUCCUGAGU ACGGCGGAAC ACGAGAAAUU CCGUCGGAAU CCGCGGGGAC CAUCCCGCAA GGCUAAAUAC UCCCUAGUGA CCGAUAGUGA ACCAGUACCG UGAGGGAAAG GUGAAAAGCA CCCCGGAAGG GGAGUGAAAU AGAUCCUGAA ACCGUGUGCC UACAACAAGU CAAAGCUCGU UAAUGAGUGA UGGCGUGCCU UUUGUAGAAU GAACCGGCGA GUUACGAUUG CAUGCGAGGU UAAGUCGAAG AGACGGAGCC GCAGCGAAAG CGAGUCUGAA UAGGGCGAAU GAGUAUGUAG UCGUAGACCC GAAACCAUGU GAUCUACCCA UGUCCAGGUU GAAGGUGCGG UAAAACGCAC UGGAGGACCG AACCCACGUA CGUUGAAAAG UGCGGGGAUG AGGUGUGGGU AGCGGAGAAA UUCCAAACGA ACUUGGAGAU AGCUGGUUCU CUCCGAAAUA GCUUUAGGGC UAGCCUCGGA AUUGAGAAUG AUGGAGGUAG AGCACUGUUU GGACUAGGGG CCCAUCUCGG GUUACCGAAU UCAGAUAAAC UCCGAAUGCC AUUCAUUUAU AUCCGGGAGU CAGACUGCGA GUGAUAAGAU CCGUAGUCGA AAGGGAAACA GCCCAGACCA CCAGCUAAGG UCCCAAAAUA UAUGUUAAGU GGAAAAGGAU GUGGGGUUGC ACAGACAACU AGGAUGUUGG CUUAGAAGCA GCCACCAUUU AAAGAGUGCG UAAUAGCUCA CUAGUCGAGU GACCCUGCGC CGAAAAUGUA CCGGGGCUAA ACAUAUUACC GAAGCUGUGG ACUACACCAU UAGGUGUAGU GGUAGGAGAG CGUUCUAAGG GCGUUGAAGG UCGAUCGUGA GGACGGCUGG AGCGCUUAGA AGUGAGAAUG CCGGUAUGAG UAGCGAAAGA CAGGUGAGAA UCCUGUCCAC CGUAUGACUA AGGUUUCCUG GGGAAGGCUC GUCCGCCCAG GGUUAGUCGG GACCUAAGCC GAGGCCGAUA GGCGUAGGCG AUGGACAACA GGUUGAUAUU CCUGUACCAG UUGUUUUUGU UUGAGCAAUG GAGGGACGCA GUAGGCUAAG GAAUGCAUGC GAUUGGAAGU GCAUGUCCAA GCAAUGAGUC UUGAGUAGAG UUAAAUGCUU UACUCUUUAA GGACAAGUUG UGACGGGGAG CGAAAUAAUA GUAGCGAAGU UCCUGACGUC ACACUGCCAA GAAAAGCUUC UAGUGAGAAA ACAACUGCCC GUACCGUAAA CCGACACAGG UAGUCGAGGA GAGUAUCCUA AGGUGAGCGA GCGAACUCUC GUUAAGGAAC UCGGCAAAAU GACCCCGUAA CUUCGGGAGA AGGGGUGCUG ACUUCGGUCA GCCGCAGUGA AUAGGCCCAA GCGACUGUUU AUCAAAAACA CAGGUCUCUG CAAAAUCGUA AGAUGAAGUA UAGGGGCUGA CGCCUGCCCG GUGCUGGAAG GUUAAGAGGA UGGGUUAGCU UCGGCGAAGC UCAGAAUUGA AGCCCCAGUA AACGGCGGCC GUAACUAUAA CGGUCCUAAG GUAGCGAAAU UCCUUGUCGG GUAAGUUCCG ACCCGCACGA AAGGCGUAAC GAUUUGGGCA CUGUCUCAAC GAGAGACUCG GUGAAAUUUU AGUACCUGUG AAGAUGCAGG UUACCCGCGA CAGGACGGAA AGACCCCAUG GAGCUUUACU GUAGUUUGAU AUUGAGUGUU UGUACCACAU GUACAGGAUA GGUAGGAGCC GAUGAGACCG GAACGCUAGU UUCGGAGGAG GCGCUGGUGG GAUACUACCC UUGUGUUAUG AACCCUCUAA CCCGCACCAC UAAUCGUGGU GGGAGACAGU GUCAGAUGGG CAGUUUGACU GGGGCGGUCG CCUCCUAAAA GGUAACGGAG GCGCCCAAAG GUUCCCUCAG AAUGGUUGGA AAUCAUUCGA AGAGUGUAAA GGCAGAAGGG AGCUUGACUG CGAGACCUAC AAGUCGAGCA GGGACGAAAG UCGGGCUUAG UGAUCCGGUG GUUCCGCAUG GAAGGGCCAU CGCUCAACGG AUAAAAGCUA CCCUGGGGAU AACAGGCUUA UCUCCCCCAA GAGUCCACAU CGACGGGGAG GUUUGGCACC UCGAUGUCGG CUCGUCGCAU CCUGGGGCUG UAGUCGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GCACGCGAGC UGGGUUCAGA ACGUCGUGAG ACAGUUCGGU CCCUAUCCGU CGCGGGCGUU GGAAAUUUGA GAGGAGCUGU CCUUAGUACG AGAGGACCGG GAUGGACUUA CCGCUGGUGU ACCAGUUGUU CUGCCAAGGG CAUUGCUGGG UAGCUAUGUA GGGAAGGGAU AAACGCUGAA AGCAUCUAAG UGUGAAGCCC ACCUCAAGAU GAGAUUUCCC AUUUCUUUAA GAAAGUAAGA CCCCUGAGAG AUGAUCAGGU AGAUAGGUUG GAAGUGGAAG GCUAGUGAUA GUUGGAGCGG ACCAAUACUA AUCGGUCGAG GACUUAAC
MassTheoretical: 942.67575 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #22: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGUGGUGGCG AUAGCGAGAA GGAUACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUU CUUAGCGCCG AUUGUAGUGA AGGGUUUCCC UUUGUGAGAG UAGGACGUCG CCACGC
MassTheoretical: 37.433188 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #23: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.159812 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #24: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.498104 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #25: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.384504 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #26: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.863113 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #27: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.164871 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #28: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.099585 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #29: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.165275 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #30: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.602868 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #31: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.960901 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #32: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.156251 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #33: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.806634 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #34: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.113282 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #35: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.542957 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #36: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.166986 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #37: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.126077 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #38: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.297111 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #39: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.892797 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #40: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.146118 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #41: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.072187 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #42: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.211366 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #43: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.234273 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #44: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.217372 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #45: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.052027 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #46: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.373507 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #47: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.466941 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #48: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.440534 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

+
Component #49: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec.

-
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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 335675
3D reconstructionSoftware: cryoSPARC / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation Coefficient / Refinement space: REAL
Input PDB model: 5LI0, 4YBB
Overall bvalue: 177
Output model

+
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