|Entry||Database: EMDB / ID: 5386|
|Title||tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex|
|Keywords||trans-translation / MLD-loading / translocation / tmRNA / EF-G / SmpB|
|Sample||Complex of 70S-tmRNA-SmpB-EF-G|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||Overall view of the 70S-tmRNA-SmpB-EF-G complex|
|Method||single particle reconstruction, at 8.3 Å resolution|
|Authors||Ramrath DJF / Yamamoto H / Rother K / Wittek D / Pech M / Mielke T / Loerke J / Scheerer P / Ivanov P / Teraoka Y / Shpanchenko O / Nierhaus KH / Spahn CMT|
|Citation||Nature, 2012, 485, 526-529|
Nature, 2012, 485, 526-529 Yorodumi Papers
|Validation Report||PDB-ID: 4v6t|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 20, 2012 / Header (metadata) release: Feb 21, 2012 / Map release: Apr 30, 2012 / Last update: Jul 23, 2014|
Downloads & links
|File||emd_5386.map.gz (map file in CCP4 format, 105470 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.26 Å|
CCP4 map header:
-Entire Complex of 70S-tmRNA-SmpB-EF-G
|Entire||Name: Complex of 70S-tmRNA-SmpB-EF-G / Details: the sample was flash frozen in liquid ethane / Number of components: 5 / Oligomeric State: Monomer|
|Mass||Theoretical: 3 MDa / Experimental: 3 MDa / Measured by: Sedimentation|
-Component #1: ribosome-prokaryote, Ribosome
|Ribosome-prokaryote||Name: Ribosome / a.k.a: 70S-tmRNA-EFG / Details: the complex was stalled with fusidic acid / Prokaryote: ALL / Recombinant expression: No|
|Mass||Theoretical: 3.05 MDa / Experimental: 3 MDa|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
|Sample solution||Specimen conc.: 0.15 mg/ml|
Buffer solution: 20 mM HEPES-KOH, pH 7.6, 4.5 mM Mg(Ac)2, 150 mM NH4Ac, 4 mM b-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
|Support film||Quantifoil R3-3 Cu 300 mesh with 2 nm carbon support film|
|Staining||flash frozen in liquid ethane|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 96.15 K / Humidity: 100 % / Method: blot for 10 seconds before plunging / Details: Vitrification instrument: FEI VITROBOT|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Dec 8, 2009|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 39000 X (nominal), 39000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm|
|Specimen Holder||Holder: Cartridge / Model: GATAN HELIUM / Temperature: 77.15 K ( 77.15 - 81.15 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 302 / Scanner: PRIMESCAN / Sampling size: 4.7 microns / Bit depth: 16|
|Processing||Method: single particle reconstruction / Number of projections: 68842 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: angular refinement / Software: Spider / CTF correction: Defocus groups / Resolution: 8.3 Å / Resolution method: FSC 0.5|
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