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- EMDB-3745: Cryo-EM structure of the foot-containing 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3745
TitleCryo-EM structure of the foot-containing 80S ribosome
Map dataProgrammed foot-containing 80S ribosome
Sample
  • Complex: Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsSarkar A / Thoms M / Barrio-Garcia C / Thomson E / Flemming D / Beckmann R / Hurt E
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control.
Authors: Anshuk Sarkar / Matthias Thoms / Clara Barrio-Garcia / Emma Thomson / Dirk Flemming / Roland Beckmann / Ed Hurt /
Abstract: Assembly of fully functional ribosomes is a prerequisite for failsafe translation. This explains why maturing preribosomal subunits have to pass through an array of quality-control checkpoints, ...Assembly of fully functional ribosomes is a prerequisite for failsafe translation. This explains why maturing preribosomal subunits have to pass through an array of quality-control checkpoints, including nuclear export, to ensure that only properly assembled ribosomes engage in translation. Despite these safeguards, we found that nuclear pre-60S particles unable to remove a transient structure composed of ITS2 pre-rRNA and associated assembly factors, termed the 'foot', escape to the cytoplasm, where they can join with mature 40S subunits to catalyze protein synthesis. However, cells harboring these abnormal ribosomes show translation defects indicated by the formation of 80S ribosomes poised with pre-60S subunits carrying tRNAs in trapped hybrid states. To overcome this translational stress, the cytoplasmic surveillance machineries RQC and Ski-exosome target these malfunctioning ribosomes. Thus, pre-60S subunits that escape nuclear quality control can enter translation, but are caught by cytoplasmic surveillance mechanisms.
History
DepositionMay 26, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 13, 2018-
UpdateJun 13, 2018-
Current statusJun 13, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0381
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0381
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3745.png

Downloads & links

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Map

FileDownload / File: emd_3745.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProgrammed foot-containing 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 416.256 Å		1.08 Å/pix.
x 384 pix.
= 416.256 Å		1.08 Å/pix.
x 384 pix.
= 416.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0381 / Movie #1: 0.0381
Minimum - Maximum-0.17333113 - 0.38821146
Average (Standard dev.)0.0012051038 (±0.03506086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 416.25598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z416.256416.256416.256
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1730.3880.001

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Supplemental data

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Sample components

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Entire : Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid

EntireName: Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid
Components
  • Complex: Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid

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Supramolecule #1: Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid

SupramoleculeName: Foot-containing 80S ribosome TAP-Flag-Nop53 Las1-HA-Aid
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2.0 nm
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 4869
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Final 3D classificationSoftware - Name: FREALIGN

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