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- EMDB-3763: Sub-tomogram average of cytosolic yeast polysomes associated with... -

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Basic information

Entry
Database: EMDB / ID: 3763
TitleSub-tomogram average of cytosolic yeast polysomes associated with mitochondria
Map dataSub-tomogram average of cytosolic yeast polysomes associated with mitochondria
SampleS. cerevisiae cytosolic polyribosome associated with mitochondria:
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsubtomogram averaging / cryo EM / 46 Å resolution
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.
Copyright: 2017 The Authors. Published under the terms of the CC BY 4.0 license.
DateDeposition: Jun 14, 2017 / Header (metadata) release: Jun 28, 2017 / Map release: Aug 30, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 143
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 143
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3763.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
6.7 Å/pix.
= 536. Å
80 pix
6.7 Å/pix.
= 536. Å
80 pix
6.7 Å/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
Contour Level:142 (by author), 143 (movie #1):
Minimum - Maximum134.00002 - 148.99998
Average (Standard dev.)140.56647 (1.3885281)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
CellA=B=C: 536 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean134.000149.000140.566

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Supplemental data

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Sample components

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Entire S. cerevisiae cytosolic polyribosome associated with mitochondria

EntireName: S. cerevisiae cytosolic polyribosome associated with mitochondria
Number of components: 1

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Component #1: protein, S. cerevisiae cytosolic polyribosome associated with mit...

ProteinName: S. cerevisiae cytosolic polyribosome associated with mitochondria
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: 7.2
VitrificationCryogen name: ETHANE
Details: blotted for ~4 s on one side in a humidified atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 5000 - 8000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: IMOD / Resolution: 46 Å / Resolution method: FSC 0.5 CUT-OFF

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