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- EMDB-21213: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-21213
TitleCryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA
Map dataSharpened cryo-EM density map
Sample
  • Complex: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 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: 2021
Title: A Time-Resolved Cryo-EM Study of Saccharomyces 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 is 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 is proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. Time-resolved cryo-electron microscopy (cryo-EM) techniques are employed 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 the computational classification approach, it is 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. The quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions.
History
DepositionJan 16, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseOct 14, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21213.png

Downloads & links

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Map

FileDownload / File: emd_21213.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM density map
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.15103571 - 0.19662005
Average (Standard dev.)0.0009289264 (±0.00914394)
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/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS276276276
D min/max/mean-0.1510.1970.001

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Supplemental data

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Additional map: Un-sharpened cryo-EM density map

Fileemd_21213_additional_1.map
AnnotationUn-sharpened cryo-EM density 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 : Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA

EntireName: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA
Components
  • Complex: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA

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Supramolecule #1: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA

SupramoleculeName: Cryo-EM reconstruction of rotated 80S ribosome bound with P/E tRNA
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: 8
GridModel: Quantifoil R2/4 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 23.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.2) / Number images used: 73418
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.2)
Final 3D classificationSoftware - Name: RELION

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