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- EMDB-4215: Yeast 80S ribosome with an uncleaved 20S rRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-4215
TitleYeast 80S ribosome with an uncleaved 20S rRNA
Map data
Sample
  • Complex: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsScaiola A / Pena C / Weisser M / Boehringer D / Leibundgut M / Klingauf-Nerurkar P / Gerhardy S / Panse VG / Ban N
CitationJournal: EMBO J / Year: 2018
Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit.
Authors: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban /
Abstract: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.
History
DepositionDec 15, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseFeb 28, 2018-
UpdateApr 11, 2018-
Current statusApr 11, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4215.png

Downloads & links

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Map

FileDownload / File: emd_4215.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum-0.36707863 - 0.6780049
Average (Standard dev.)0.002341078 (±0.023977578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.3670.6780.002

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Supplemental data

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Half map: #1

Fileemd_4215_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4215_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA

EntireName: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA
Components
  • Complex: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA

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Supramolecule #1: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA

SupramoleculeName: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA
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: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 145081
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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