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- EMDB-3762: Sub-tomogram average of the cytosolic yeast ribosome associated w... -

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Basic information

Entry
Database: EMDB / ID: EMD-3762
TitleSub-tomogram average of the cytosolic yeast ribosome associated with mitochondria
Map dataSub-tomogram average of the cytosolic yeast ribosome bound to mitochondria
Sample
  • Complex: S. cerevisiae cytosolic ribosome associated with mitochondria
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 38.0 Å
AuthorsGold VAM / Chroscicki P / Bragoszewski P / Chacinska A
CitationJournal: EMBO Rep / Year: 2017
Title: Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography.
Authors: Vicki Am Gold / Piotr Chroscicki / Piotr Bragoszewski / Agnieszka Chacinska /
Abstract: We employed electron cryo-tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation-arrested ribosomes reveal the clustered organization of the TOM complex, ...We employed electron cryo-tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation-arrested ribosomes reveal the clustered organization of the TOM complex, corroborating earlier reports of localized translation. Ribosomes are shown to interact specifically with the TOM complex, and nascent chain binding is crucial for ribosome recruitment and stabilization. Ribosomes are bound to the membrane in discrete clusters, often in the vicinity of the crista junctions. This interaction highlights how protein synthesis may be coupled with transport. Our work provides unique insights into the spatial organization of cytosolic ribosomes on mitochondria.
History
DepositionJun 14, 2017-
Header (metadata) releaseJun 28, 2017-
Map releaseAug 30, 2017-
UpdateOct 11, 2017-
Current statusOct 11, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 140.311213094
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 140.311213094
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3762.png

Downloads & links

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Map

FileDownload / File: emd_3762.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the cytosolic yeast ribosome bound to mitochondria
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.7 Å/pix.
x 80 pix.
= 536. Å		6.7 Å/pix.
x 80 pix.
= 536. Å		6.7 Å/pix.
x 80 pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 140. / Movie #1: 140.3112131
Minimum - Maximum131.999979999999994 - 149.
Average (Standard dev.)138.66837000000001 (±1.1503549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.76.76.7
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean132.000149.000138.668

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Supplemental data

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Sample components

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Entire : S. cerevisiae cytosolic ribosome associated with mitochondria

EntireName: S. cerevisiae cytosolic ribosome associated with mitochondria
Components
  • Complex: S. cerevisiae cytosolic ribosome associated with mitochondria

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Supramolecule #1: S. cerevisiae cytosolic ribosome associated with mitochondria

SupramoleculeName: S. cerevisiae cytosolic ribosome associated with mitochondria
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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE
Details: blotted for ~4 s on one side in a humidified atmosphere.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm
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: 38.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD (ver. 4.8.46) / Number subtomograms used: 1215
ExtractionNumber tomograms: 23 / Number images used: 1215
CTF correctionSoftware - Name: IMOD (ver. 4.8.46)
Final angle assignmentType: NOT APPLICABLE

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