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- EMDB-4641: Structure of a bacterial 70S ribosomal subunit in complex with ca... -

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Basic information

Entry
Database: EMDB / ID: EMD-4641
TitleStructure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit
Map data
Sample
  • Complex: Structure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsScaiola A / Leibundgut M / Boehringer D / Ritz D
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic.
Authors: Alain Scaiola / Marc Leibundgut / Daniel Boehringer / Patrick Caspers / Daniel Bur / Hans H Locher / Georg Rueedi / Daniel Ritz /
Abstract: Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl ...Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with the peptidyl transferase reaction. Cadazolid is the first member of quinoxolidinone antibiotics, which are characterized by combining the pharmacophores of oxazolidinones and fluoroquinolones, and it is evaluated for treatment of Clostridium difficile gastrointestinal infections that frequently occur in hospitalized patients. In vitro protein synthesis inhibition by cadazolid was shown in Escherichia coli and Staphylococcus aureus, including an isolate resistant against linezolid, the prototypical oxazolidinone antibiotic. To better understand the mechanism of inhibition, we determined a 3.0 Å cryo-electron microscopy structure of cadazolid bound to the E. coli ribosome in complex with mRNA and initiator tRNA. Here we show that cadazolid binds with its oxazolidinone moiety in a binding pocket in close vicinity of the PTC as observed previously for linezolid, and that it extends its unique fluoroquinolone moiety towards the A-site of the PTC. In this position, the drug inhibits protein synthesis by interfering with the binding of tRNA to the A-site, suggesting that its chemical features also can enable the inhibition of linezolid-resistant strains.
History
DepositionFeb 27, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4641.png

Downloads & links

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Map

FileDownload / File: emd_4641.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.12 Å		1.08 Å/pix.
x 290 pix.
= 312.91 Å		1.08 Å/pix.
x 290 pix.
= 312.91 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.045
Minimum - Maximum-0.10092925 - 0.22667907
Average (Standard dev.)0.0009855794 (±0.008579834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290280
Spacing290290280
CellA: 312.91 Å / B: 312.91 Å / C: 302.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0791.0791.079
M x/y/z290290280
origin x/y/z0.0000.0000.000
length x/y/z312.910312.910302.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290280
D min/max/mean-0.1010.2270.001

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Supplemental data

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Mask #1

Fileemd_4641_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4641_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4641_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of a bacterial 70S ribosomal subunit in complex with ca...

EntireName: Structure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit
Components
  • Complex: Structure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit

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Supramolecule #1: Structure of a bacterial 70S ribosomal subunit in complex with ca...

SupramoleculeName: Structure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Escherichia coli (E. coli)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ybb

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 59148
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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