|Entry||Database: EMDB / ID: 1484|
|Title||Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation|
|Keywords||ribosome / secY / translocation / electron microscopy|
|Sample||Ribosome SecY complex|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||Escherichia coli ribosome secY complex|
|Method||single particle reconstruction, at 9.6 Å resolution|
|Authors||Menetret JF / Schaletzky J / Clemons WM Jr / Osborne AR / Skanland SS / Denison C / Gygi SP / Kirkpatrick DS / Park E / Ludtke SJ / Rapoport TA / Akey CW|
|Citation||Mol. Cell, 2007, 28, 1083-1092|
Mol. Cell, 2007, 28, 1083-1092 Yorodumi Papers
|Validation Report||PDB-ID: 3bo0|
About validation report
|Date||Deposition: Feb 26, 2008 / Header (metadata) release: Feb 26, 2008 / Map release: May 29, 2009 / Last update: Oct 24, 2012|
Downloads & links
|File||emd_1484.map.gz (map file in CCP4 format, 11665 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.73 Å|
CCP4 map header:
-Entire Ribosome SecY complex
|Entire||Name: Ribosome SecY complex / Number of components: 1 / Oligomeric State: monomer|
|Mass||Theoretical: 3.2 MDa|
-Component #1: ribosome-prokaryote, 70S ribosome
|Ribosome-prokaryote||Name: 70S ribosome / a.k.a: ribosome / Prokaryote: ALL / Recombinant expression: No|
|Mass||Theoretical: 3.2 MDa|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Sample solution||Specimen conc.: 0.3 mg/ml|
Buffer solution: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM
|Support film||400 mesh Cu grids with continuous carbon film|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 95 % / Method: 1 second blot / Details: Vitrification instrument: home-made|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20|
Details: About 30 percent of the data were collected at 30 degree tilt and micrographs were processed in small strips parallel to the tilt axis to correct for the defocus ramp.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 51000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm|
|Specimen Holder||Holder: eucentric / Model: GATAN LIQUID NITROGEN / Tilt Angle: 0 - 30 deg. / Temperature: 90 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 351 / Scanner: OTHER / Sampling size: 4.5 microns / Bit depth: 16 / OD range: 1 / Details: Creoscitex Eversmart scanner was used|
|Processing||Method: single particle reconstruction / Number of projections: 39000 / Details: 1900 classes were used in EMAN 3D refinement / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: projection matching / Software: EMAN / CTF correction: by micrograph / Resolution: 9.6 Å / Resolution method: FSC 0.5|
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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