|Entry||Database: EMDB / ID: 1924|
|Title||Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates|
|Keywords||pre-40S / 40S intermediate / Ltv1 deletion|
|Sample||S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion|
|Source||Saccharomyces cerevisiae / yeast / Bakers' yeast / サッカロミセス・セレビシエ /|
|Map data||Surface rendered Ltv1 deletion map|
|Method||single particle reconstruction, at 20 Å resolution|
|Authors||Strunk BS / Loucks CR / Su M / Vashisth H / Cheng S / Schilling J / BrooksIII CL / Karbstein K / Skiniotis G|
|Citation||Science, 2011, 333, 1449-1453|
Science, 2011, 333, 1449-1453 Yorodumi Papers
|Date||Deposition: Jul 5, 2011 / Header (metadata) release: Nov 4, 2011 / Map release: Nov 4, 2011 / Last update: Oct 10, 2012|
Downloads & links
|File||emd_1924.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.24 Å|
CCP4 map header:
-Entire S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
|Entire||Name: S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion|
Details: Monodisperse / Number of components: 1
|Mass||Theoretical: 1.4 MDa|
-Component #1: ribosome-eukaryote, pre-40S
|Ribosome-eukaryote||Name: pre-40S / a.k.a: pre-40S / Eukaryote: SSU 40S / Recombinant expression: No|
|Mass||Theoretical: 1.4 MDa|
|Source||Species: Saccharomyces cerevisiae / yeast / Bakers' yeast / サッカロミセス・セレビシエ /|
|Sample solution||Specimen conc.: 1.5 mg/ml|
Buffer solution: 50mM Tris-Cl, 100mM NaCl, 10mM MgCl2, 0.075% NP40, 1mM imidazole, 2mM EGTA, 10 mM BME
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 100 % / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 66964 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4000 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: OTHER / Temperature: 89 K ( 89 - 89 K)
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 350 / Sampling size: 2.24 microns|
|Processing||Method: single particle reconstruction / Number of projections: 10235 / Details: Manual particle selection / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Projection matching / Euler angles: EMAN convention / Software: EMAN / CTF correction: Each micrograph / Details: Final map was filtered to 20A resolution / Resolution: 20 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: NAMD / Refinement protocol: flexible / Target criteria: CC / Refinement space: REAL / Details: Protocol: MDFF|
Input PDB model: 3O2Z
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