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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12064 | ||||||||||||||||||
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Title | Yeast 80S ribosome bound to eEF3 and P/P-tRNA (POST-3) | ||||||||||||||||||
![]() | Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (postprocessed masked) | ||||||||||||||||||
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Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||
![]() | Ranjan N / Pochopien AA / Wu CC / Beckert B / Blanchet S / Green R / Rodnina MV / Wilson DN | ||||||||||||||||||
Funding support | 5 items
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![]() | ![]() Title: Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation. Authors: Namit Ranjan / Agnieszka A Pochopien / Colin Chih-Chien Wu / Bertrand Beckert / Sandra Blanchet / Rachel Green / Marina V Rodnina / Daniel N Wilson / ![]() ![]() Abstract: In addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the ...In addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the ribosomal A and E sites, its exact mechanism of action is unclear. Here, we show that eEF3 acts at the mRNA-tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. Depletion of eEF3 in vivo leads to a general slowdown in translation elongation due to accumulation of ribosomes with an occupied A site. Cryo-EM analysis of native eEF3-ribosome complexes shows that eEF3 facilitates late steps of translocation by favoring non-rotated ribosomal states, as well as by opening the L1 stalk to release the E-site tRNA. Additionally, our analysis provides structural insights into novel translation elongation states, enabling presentation of a revised yeast translation elongation cycle. | ||||||||||||||||||
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 | ![]() | 21.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.4 KB 15.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 199.7 KB | ||
Others | ![]() ![]() ![]() | 224.8 MB 225.7 MB 225.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | 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
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Annotation | Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (postprocessed masked) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM structure of the S. cerevisiae 80S ribosome...
File | emd_12064_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of the S. cerevisiae 80S ribosome...
File | emd_12064_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of the S. cerevisiae 80S ribosome...
File | emd_12064_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (half map 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of the S. cerevisiae 80S ribosome in complex wi...
Entire | Name: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and A/A- and P/P-site tRNAs. |
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Components |
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-Supramolecule #1: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex wi...
Supramolecule | Name: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and A/A- and P/P-site tRNAs. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |