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Yorodumi- EMDB-17145: polysome/di-ribosome class III in chloramphenicol-treated Mycopla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17145 | |||||||||
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Title | polysome/di-ribosome class III in chloramphenicol-treated Mycoplasma pneumoniae cells | |||||||||
Map data | ||||||||||
Sample |
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Keywords | In situ / cryo-electron tomography / bacterial ribosome / Chloramphenicol / antibiotic / polysome / RIBOSOME | |||||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit / protein transport / protein folding / regulation of translation / large ribosomal subunit rRNA binding / transferase activity / small ribosomal subunit / ribosomal large subunit assembly ...peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit / protein transport / protein folding / regulation of translation / large ribosomal subunit rRNA binding / transferase activity / small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cell division / response to antibiotic / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycoplasmoides pneumoniae M129 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Xue L / Spahn C / Schacherl M / Mahamid J | |||||||||
Funding support | United States, Germany, 2 items
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Citation | Journal: To Be Published 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 | emd_17145.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-17145-v30.xml emd-17145.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17145_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_17145.png | 78 KB | ||
Masks | emd_17145_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-17145.cif.gz | 4.9 KB | ||
Others | emd_17145_half_map_1.map.gz emd_17145_half_map_2.map.gz | 49.7 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17145 | HTTPS FTP |
-Validation report
Summary document | emd_17145_validation.pdf.gz | 955.1 KB | Display | EMDB validaton report |
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Full document | emd_17145_full_validation.pdf.gz | 954.6 KB | Display | |
Data in XML | emd_17145_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_17145_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17145 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17145 | HTTPS FTP |
-Related structure data
Related structure data | 8p8vM 8p8wM M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17145.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17145_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17145_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17145_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Mycoplasmoides pneumoniae M129 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-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. |
-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: FIELD EMISSION GUN |
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 |