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- EMDB-4330: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4330 | |||||||||
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Title | Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (Map A) | |||||||||
![]() | For optimal visualization of all tRNA, eIF2 gamma and eIF3 PCI domains, gauss-filter the map by 1.1 and display it at 0.02 contour level. | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||
![]() | Llacer JL / Hussain T / Gordiyenko Y / Ramakrishnan V | |||||||||
![]() | ![]() 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 / ![]() ![]() ![]() ![]() Abstract: In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) ...In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNA. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNA interaction influenced initiation at near-cognate UUG codons and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 94.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
Images | ![]() | 222.4 KB | ||
Others | ![]() ![]() | 90.6 MB 90.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4327C ![]() 4328C ![]() 4329C ![]() 4331C ![]() 6fyxC ![]() 6fyyC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | For optimal visualization of all tRNA, eIF2 gamma and eIF3 PCI domains, gauss-filter the map by 1.1 and display it at 0.02 contour level. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4330_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4330_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-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 A) |
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Components |
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-Supramolecule #1: Structure of a partial yeast 48S preinitiation complex with eIF5 ...
Supramolecule | Name: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model A) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#47 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.8 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.15 mg/mL | ||||||||||||||||||
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Buffer | pH: 6.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 3 / Number real images: 3600 / Average exposure time: 1.1 sec. / Average electron dose: 40.0 e/Å2 Details: Images were collected in movie-mode at 32 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 66 / Target criteria: FSC |
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