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- EMDB-12064: Yeast 80S ribosome bound to eEF3 and P/P-tRNA (POST-3) -

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Basic information

Entry
Database: EMDB / ID: EMD-12064
TitleYeast 80S ribosome bound to eEF3 and P/P-tRNA (POST-3)
Map dataCryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (postprocessed masked)
Sample
  • Complex: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and A/A- and P/P-site tRNAs.
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRanjan N / Pochopien AA / Wu CC / Beckert B / Blanchet S / Green R / Rodnina MV / Wilson DN
Funding support5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission2643
Howard Hughes Medical Institute (HHMI)
German Research Foundation (DFG)3194/1-1
Leibniz Association
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM059425
CitationJournal: EMBO J / Year: 2021
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
DepositionDec 9, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0316
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0316
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12064.png

Downloads & links

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Map

FileDownload / File: emd_12064.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (postprocessed masked)
Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.0316 / Movie #1: 0.0316
Minimum - Maximum-0.16033293 - 0.22132182
Average (Standard dev.)0.0008446988 (±0.008897021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 455.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z455.280455.280455.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1600.2210.001

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Supplemental data

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Additional map: Cryo-EM structure of the S. cerevisiae 80S ribosome...

Fileemd_12064_additional_1.map
AnnotationCryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the S. cerevisiae 80S ribosome...

Fileemd_12064_half_map_1.map
AnnotationCryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the S. cerevisiae 80S ribosome...

Fileemd_12064_half_map_2.map
AnnotationCryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and P/P-site tRNA (half map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the S. cerevisiae 80S ribosome in complex wi...

EntireName: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex with eEF3 and A/A- and P/P-site tRNAs.
Components
  • Complex: 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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Supramolecule #1: Cryo-EM structure of the S. cerevisiae 80S ribosome in complex wi...

SupramoleculeName: 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

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12589
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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