|Entry||Database: EMDB / ID: 4331|
|Title||Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (Map B)|
|Map data||For optimal visualization of all tRNA, eIF2 gamma and eIF3b and eIF3i beta propellers, gauss-filter the map by 1.2 and display it at 0.02 contour level.|
|Sample||Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B):|
|Source||Kluyveromyces lactis (yeast)|
|Method||single particle reconstruction / cryo EM / 3.5 Å resolution|
|Authors||Llacer JL / Hussain T / Gordiyenko Y / Ramakrishnan V|
|Citation||Journal: Elife / Year: 2018|
Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
Authors: Jose Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan
|Date||Deposition: Mar 12, 2018 / Header (metadata) release: Aug 24, 2016 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4331.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.34 Å|
CCP4 map header:
-Entire Structure of a partial yeast 48S preinitiation complex with eIF5 ...
|Entire||Name: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B)|
Number of components: 1
-Component #1: protein, Structure of a partial yeast 48S preinitiation complex w...
|Protein||Name: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model B)|
Recombinant expression: No
|Mass||Theoretical: 1.8 MDa|
|Source||Species: Kluyveromyces lactis (yeast)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.15 mg/ml / pH: 6.5|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 78000.0 X (nominal), 104478.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm|
|Specimen Holder||Model: OTHER / Temperature: K ( 90.0 - 100.0 K)|
|Camera||Detector: FEI FALCON III (4k x 4k)|
|Image acquisition||Number of digital images: 3600|
Details: Images were collected in movie-mode at 32 frames per second
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 54699 / Details: FEI Falcon III|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Target criteria: FSC / Refinement space: RECIPROCAL / Overall bvalue: 54|
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