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- EMDB-21218: Cryo-EM reconstruction of incomplete 80S ribosome (class v) -

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Basic information

Entry
Database: EMDB / ID: EMD-21218
TitleCryo-EM reconstruction of incomplete 80S ribosome (class v)
Map dataCryo-EM reconstruction of incomplete 80S ribosome (class v)
Sample
  • Complex: Cryo-EM reconstruction of incomplete 80S ribosome (class v)
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.8 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • 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_21218.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of incomplete 80S ribosome (class v)
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.03164056 - 0.06610231
Average (Standard dev.)0.00019005766 (±0.005876003)
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-0.0320.0660.000

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Supplemental data

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Additional map: Un-sharpened cryo-EM density map

Fileemd_21218_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 v)

EntireName: Cryo-EM reconstruction of incomplete 80S ribosome (class v)
Components
  • Complex: Cryo-EM reconstruction of incomplete 80S ribosome (class v)

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Supramolecule #1: Cryo-EM reconstruction of incomplete 80S ribosome (class v)

SupramoleculeName: Cryo-EM reconstruction of incomplete 80S ribosome (class v)
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 23.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.2) / Number images used: 7081
FSC plot (resolution estimation)

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