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- EMDB-21888: Structure of the 50S subunit of the ribosome from Methicillin Res... -

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Basic information

Entry
Database: EMDB / ID: EMD-21888
TitleStructure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with an isomer of the tedizolid
Map data
Sample50S ribosomal subunitProkaryotic large ribosomal subunit:
(50S ribosomal protein ...) x 25 / uL25 / (nucleic-acidNucleic acid) x 2 / ligand
Function / homology
Function and homology information


ribosome assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / negative regulation of translation / tRNA binding ...ribosome assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / RNA binding
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L25, C-terminal / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L25, C-terminal / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L19, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L19 signature. / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L27 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / 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 L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L21 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L32p / Ribosomal prokaryotic L21 protein / Ribosomal protein L21-like / L21-like superfamily / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / 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 L2 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L14 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L2, domain 3 / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily
Similarity search - Domain/homology
50S ribosomal protein L16 / 50S ribosomal protein L27 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L36 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 50S ribosomal protein L35 ...50S ribosomal protein L16 / 50S ribosomal protein L27 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L36 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 50S ribosomal protein L35 / 50S ribosomal protein L20 / 50S ribosomal protein L21 / 50S ribosomal protein L19 / 50S ribosomal protein L33 2 / 50S ribosomal protein L28 / 50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L34 / 50S ribosomal protein L24 / 50S ribosomal protein L18 / 50S ribosomal protein L23 / 50S ribosomal protein L13 / 50S ribosomal protein L3 / 50S ribosomal protein L6 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 50S ribosomal protein L22 / 50S ribosomal protein L16 / 50S ribosomal protein L17 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L22 / 50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 50S ribosomal protein L14 / 50S ribosomal protein L19 / 50S ribosomal protein L33 / 50S ribosomal protein L20 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 50S ribosomal protein L21 / 50S ribosomal protein L4 / 50S ribosomal protein L29 / 50S ribosomal protein L25 / 50S ribosomal protein L15 / 50S ribosomal protein L30 / 50S ribosomal protein L2 / 50S ribosomal protein L34 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L30
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBelousoff MJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH1910126 United States
CitationJournal: ACS Pharmacol Transl Sci / Year: 2020
Title: Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.
Authors: Alexander Wright / Kieran Deane-Alder / Edward Marschall / Rebecca Bamert / Hari Venugopal / Trevor Lithgow / David W Lupton / Matthew J Belousoff /
Abstract: Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the ...Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity. Consequently, the structure-activity relationship around the core oxazolidinone is constantly evolving, often reflected with new structural motifs present in nascent oxazolidinones. Herein we describe the use of cryo-electron microscopy to examine the differences in binding of several functionally different oxazolidinones in the hopes of enhanced understanding of their SAR. Tedizolid, radezolid, T145, and contezolid have been examined within the peptidyl transferase center (PTC) of the 50S ribosomal subunit from methicillin resistant . The ribosome-antibiotic complexes were resolved to a resolution of around 3 Å enabling unambiguous assignment of how each antibiotic interacts with the PTC.
History
DepositionApr 30, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by height
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-6wru
  • Surface level: 1
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21888.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 432 pix.
= 419.04 Å
0.97 Å/pix.
x 432 pix.
= 419.04 Å
0.97 Å/pix.
x 432 pix.
= 419.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 1
Minimum - Maximum-7.6037693 - 11.419257
Average (Standard dev.)0.013022026 (±0.29172757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 419.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.970.970.97
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z419.040419.040419.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-7.60411.4190.013

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Supplemental data

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Half map: #2

Fileemd_21888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_21888_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 50S ribosomal subunit

EntireName: 50S ribosomal subunitProkaryotic large ribosomal subunit
Number of components: 30

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Component #1: protein, 50S ribosomal subunit

ProteinName: 50S ribosomal subunitProkaryotic large ribosomal subunit
Recombinant expression: No
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #2: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.392771 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #3: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.217164 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #4: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.720295 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #5: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.700483 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #6: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.871947 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #7: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.627328 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #8: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.59153 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #9: protein, uL25

ProteinName: uL25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.063077 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #10: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.967235 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #11: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.49182 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #12: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.459922 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #13: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.434487 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #14: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.472556 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #15: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.885783 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #16: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.0644 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #17: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.593188 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #18: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.318422 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #19: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.523752 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #20: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.517219 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #21: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.359427 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #22: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.157342 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #23: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.62889 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #24: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.274049 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #25: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.771773 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #26: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.124093 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #27: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGUA AGUAAGCUUU GAUCCAGAGA UUUCCGAAUG GGGAAACCCA GCAUGAGUUA UGUCAUGUUA UCGAUAUGUG AAUACAUAGC ...Sequence:
GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGUA AGUAAGCUUU GAUCCAGAGA UUUCCGAAUG GGGAAACCCA GCAUGAGUUA UGUCAUGUUA UCGAUAUGUG AAUACAUAGC AUAUCAGAAG GCACACCCGG AGAACUGAAA CAUCUUAGUA CCCGGAGGAA GAGAAAGAAA AUUCGAUUCC CUUAGUAGCG GCGAGCGAAA CGGGAAGAGC CCAAACCAAC AAGCUUGCUU GUUGGGGUUG UAGGACACUC UAUACGGAGU UACAAAGGAC GACAUUAGAC GAAUCAUCUG GAAAGAUGAA UCAAAGAAGG UAAUAAUCCU GUAGUCGAAA AUGUUGUCUC UCUUGAGUGG AUCCUGAGUA CGACGGAGCA CGUGAAAUUC CGUCGGAAUC UGGGAGGACC AUCUCCUAAG GCUAAAUACU CUCUAGUGAC CGAUAGUGAA CCAGUACCGU GAGGGAAAGG UGAAAAGCAC CCCGGAAGGG GAGUGAAAUA GAACCUGAAA CCGUGUGCUU ACAAGUAGUC AGAGCCCGUU AAUGGGUGAU GGCGUGCCUU UUGUAGAAUG AACCGGCGAG UUACGAUUUG AUGCAAGGUU AAGCAGUAAA UGUGGAGCCG UAGCGAAAGC GAGUCUGAAU AGGGCGUUUA GUAUUUGGUC GUAGACCCGA AACCAGGUGA UCUACCCUUG GUCAGGUUGA AGUUCAGGUA ACACUGAAUG GAGGACCGAA CCGACUUACG UUGAAAAGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGGGCUA GCCUCAAGUG AUGAUUAUUG GAGGUAGAGC ACUGUUUGGA CGAGGGGCCC CUCUCGGGUU ACCGAAUUCA GACAAACUCC GAAUGCCAAU UAAUUUAACU UGGGAGUCAG AACAUGGGUG AUAAGGUCCG UGUUCGAAAG GGAAACAGCC CAGACCACCA GCUAAGGUCC CAAAAUAUAU GUUAAGUGGA AAAGGAUGUG GCGUUGCCCA GACAACUAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAGUGCGUAA UAGCUCACUA GUCGAGUGAC ACUGCGCCGA AAAUGUACCG GGGCUAAACA UAUUACCGAA GCUGUGGAUU GUCCUUUGGA CAAUGGUAGG AGAGCGUUCU AAGGGCGUUG AAGCAUGAUC GUAAGGACAU GUGGAGCGCU UAGAAGUGAG AAUGCCGGUG UGAGUAGCGA AAGACGGGUG AGAAUCCCGU CCACCGAUUG ACUAAGGUUU CCAGAGGAAG GCUCGUCCGC UCUGGGUUAG UCGGGUCCUA AGCUGAGGCC GACAGGCGUA GGCGAUGGAU AACAGGUUGA UAUUCCUGUA CCACCUAUAA UCGUUUUAAU CGAUGGGGGG ACGCAGUAGG AUAGGCGAAG CGUGCGAUUG GAUUGCACGU CUAAGCAGUA AGGCUGAGUA UUAGGCAAAU CCGGUACUCG UUAAGGCUGA GCUGUGAUGG GGAGAAGACA UUGUGUCUUC GAGUCGUUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGAGAAU UCUAAGGUGA GCGAGCGAAC UCUCGUUAAG GAACUCGGCA AAAUGACCCC GUAACUUCGG GAGAAGGGGU GCUCUUUAGG GUUAACGCCC AGAAGAGCCG CAGUGAAUAG GCCCAAGCGA CUGUUUAUCA AAAACACAGG UCUCUGCUAA ACCGUAAGGU GAUGUAUAGG GGCUGACGCC UGCCCAGUGC UGGAAGGUUA AGAGGAGUGG UUAGCUUCUG CGAAGCUACG AAUCGAAGCC CCAGUAAACG GCGGCCGUAA CUAUAACGGU CCUAAGGUAG CGAAAUUCCU UGUCGGGUAA GUUCCGACCC GCACGAAAGG CGUAACGAUU UGGGCACUGU CUCAACGAGA GACUCGGUGA AAUCAUAGUA CCUGUGAAGA UGCAGGUUAC CCGCGACAGG ACGGAAAGAC CCCGUGGAGC UUUACUGUAG CCUGAUAUUG AAAUUCGGCA CAGCUUGUAC AGGAUAGGUA GGAGCCUUUG AAACGUGAGC GCUAGCUUAC GUGGAGGCGC UGGUGGGAUA CUACCCUAGC UGUGUUGGCU UUCUAACCCG CACCACUUAU CGUGGUGGGA GACAGUGUCA GGCGGGCAGU UUGACUGGGG CGGUCGCCUC CUAAAAGGUA ACGGAGGCGC UCAAAGGUUC CCUCAGAAUG GUUGGAAAUC AUUCAUAGAG UGUAAAGGCA UAAGGGAGCU UGACUGCGAG ACCUACAAGU CGAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGCUACCCC GGGGAUAACA GGCUUAUCUC CCCCAAGAGU UCACAUCGAC GGGGAGGUUU GGCACCUCGA UGUCGGCUCA UCGCAUCCUG GGGCUGUAGU CGGUCCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGUAC GCGAGCUGGG UUCAGAACGU CGUGAGACAG UUCGGUCCCU AUCCGUCGUG GGCGUAGGAA AUUUGAGAGG AGCUGUCCUU AGUACGAGAG GACCGGGAUG GACAUACCUC UGGUGUACCA GUUGUCGUGC CAACGGCAUA GCUGGGUAGC UAUGUGUGGA CGGGAUAAGU GCUGAAAGCA UCUAAGCAUG AAGCCCCCCU CAAGAUGAGA UUUCCCAACU UCGGUUAUAA GAUCCCUCAA AGAUGAUGAG GUUAAUAGGU UCGAGGUGGA AGCAUGGUGA CAUGUGGAGC UGACGAAUAC UAAUCGAUCG AAGACUUAAU CAA
MassTheoretical: 946.680625 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #28: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGACG AUGGUAGUCC AACUUACGUU CCGCUAGAGU AGAACGUUCC AGGGC
MassTheoretical: 36.957961 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #29: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.198369 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #30: ligand, Tedizolid isomer

LigandName: Tedizolid isomer / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.370338 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 77500
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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