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- EMDB-21215: Cryo-EM reconstruction of incomplete 80S ribosome (class ii) -

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Basic information

Entry
Database: EMDB / ID: EMD-21215
TitleCryo-EM reconstruction of incomplete 80S ribosome (class ii)
Map data
SampleCryo-EM reconstruction of incomplete 80S ribosome (class ii)
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsFrank J / Sun M / Shen B / Li W
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM29169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HL68744 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64779 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)CA098131 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)ES11993 United States
CitationJournal: Proteomics / Year: 2020
Title: A time-resolved cryo-EM Study of S. cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source.
Authors: Ming Sun / Bingxin Shen / Wen Li / Parimal Samir / Christopher M Browne / Andrew J Link / Joachim Frank /
Abstract: The role of the ribosome in the regulation of gene expression has come into increased focus. It has been proposed that ribosomes are catalytic engines capable of changing their protein composition in ...The role of the ribosome in the regulation of gene expression has come into increased focus. It has been proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. We employed time-resolved cryo-electron microscopy (cryo-EM) techniques to identify quantitative changes in the protein composition and structure of the Saccharomyces cerevisiae 80S ribosomes after shifting the carbon source from glucose to glycerol. Using cryo-EM combined with our computational classification approach, we found that a fraction of the yeast cells' 80S ribosomes lack ribosomal proteins at the entrance and exit sites for tRNAs, including uL16(RPL10), eS1(RPS1), uS11(RPS14A/B)) and eS26(RPS26A/B). This fraction increased after a change from glucose to glycerol medium. Our quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions. This article is protected by copyright. All rights reserved.
History
DepositionJan 16, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21215.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 276 pix.
= 458.16 Å
1.66 Å/pix.
x 276 pix.
= 458.16 Å
1.66 Å/pix.
x 276 pix.
= 458.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.09735058 - 0.13606358
Average (Standard dev.)0.00091851276 (±0.007394048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions276276276
Spacing276276276
CellA=B=C: 458.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z276276276
origin x/y/z0.0000.0000.000
length x/y/z458.160458.160458.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS276276276
D min/max/mean-0.0970.1360.001

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Supplemental data

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Additional map: Un-sharpened cryo-EM density map

Fileemd_21215_additional_1.map
AnnotationUn-sharpened cryo-EM density map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Cryo-EM reconstruction of incomplete 80S ribosome (class ii)

EntireName: Cryo-EM reconstruction of incomplete 80S ribosome (class ii)
Number of components: 1

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Component #1: protein, Cryo-EM reconstruction of incomplete 80S ribosome (class ii)

ProteinName: Cryo-EM reconstruction of incomplete 80S ribosome (class ii)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 23 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 32277
3D reconstructionSoftware: RELION / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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