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- EMDB-17141: 70S ribosome with EF-Tu-tRNA, P and E-site tRNAs in chloramphenic... -
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Open data
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Basic information
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Title | 70S ribosome with EF-Tu-tRNA, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data | |||||||||
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![]() | In situ / cryo-electron tomography / bacterial ribosome / Chloramphenicol / antibiotic / RIBOSOME | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Xue L / Spahn C / Schacherl M / Mahamid J | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural evidence of context-dependent action of chloramphenicol in cells Authors: Xue L / Spahn C / Schacherl M / Mahamid J | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 223.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() | 49.7 MB 49.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.7005 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mycoplasma pneumoniae M129 cells treated with chloramphenicol
Entire | Name: Mycoplasma pneumoniae M129 cells treated with chloramphenicol |
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Components |
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-Supramolecule #1: Mycoplasma pneumoniae M129 cells treated with chloramphenicol
Supramolecule | Name: Mycoplasma pneumoniae M129 cells treated with chloramphenicol type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 Details: Modified Hayflick medium: 14.7g/l Difco PPLO(Becton Dickinson), 20% (v/v) Gibco horse serum (New Zealand origin), 100 mM HEPES-Na; pH 7.4, 1% (w/w) glucose, 0.002% (w/w) phenol red, 1000 U/ml penicillin G. |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber.. |
Details | Mycoplasma pneumoniae M129 cells were grown on gold Quantifoil grids at 37 Celsius in modified Hayflick medium. Treatment with chloramphenicol at a final concentration of 0.2 mg/ml was performed for approximately 15 minutes before plunge freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.34 e/Å2 Details: Gatan K3 camera in non-CDS counting mode, targeted dose rate on camera ~20 e/pixel/second, 10 frames per tilt image, constant exposure time for each tilt, pixel size 1.329A |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.25 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |