EMPIAR-12534 - Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import [multiple data sets in TIFF and MRC formats]

EMPIAR-12534

Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import [multiple data sets in TIFF and MRC formats]

Publication:

Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import

Chang YT, Barad BA, Rahmani H, Zid BM, Grotjahn DA

bioRxiv (2024)

PMID: 39071314

DOI: 10.1101/2024.07.17.604013

Related EMDB entry:

EMD-48751 EMD-48752

Deposited:

2025-01-10

Released:

2025-03-17

Last modified:

2025-03-17

Imageset size:

764.19 GB

Imageset DOI:

10.6019/EMPIAR-12534

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Raw unaligned frame and metadata for each tilt in tilt-series acquired on CHX-treated S. cerevisiae cryo-FIB lamellae

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

462

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.663, 1.663)

Details:

Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding count reference files (mrc file) are in the subfolders of the EMPIAR_upload/Frames folder. The number of frames per image varies from 38 to 42. Subfolder names with YTC041_1, YTC041_2, and YTC042_2 are datasets acquired on S. cerevisiae grown in YPG. Subfolder names with YTC043_1 and YTC043_2 are datasets acquired on S. cerevisiae grown in YPD.

Files:

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2. Unaligned tilt series stack of cryo-electron tomography acquired on CHX-treated S. cerevisiae cryo-FIB lamellae

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.663, 1.663)

Details:

The tilt series stacks (.st file) and rawtlt files (in Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the EMPIAR_upload/PACE_mdoc folder. Tilt series stacks are then aligned in IMOD.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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3. Reconstructed tomograms of CHX-treated S. cerevisiae lamellae used for segmentation of mitochondria

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(682, 960)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(9.98, 9.98)

Details:

Bin6 tomograms are reconstructed from Warp after IMOD alignment. The coordinates of 80S ribosome and co-translating ribosome are provided in the EMPIAR_upload/Particle_lists folder.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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4. Raw unaligned frame and metadata for each tilt in tilt-series acquired on vehicle-treated S. cerevisiae cryo-FIB lamellae

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

492

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.638, 2.638)

Details:

Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding count reference files (mrc file) are in the subfolders of the EMPIAR_upload_nonCHX/Frames folder. The number of frames per image varies from 39 to 41. Subfolder name with YTC009_3 is the dataset acquired on S. cerevisiae grown in YPG, and subfolder name with YTC025_2 is the dataset acquired on S. cerevisiae grown in YPD.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

5. Unaligned tilt series stack of cryo-electron tomography acquired on vehicle-treated S. cerevisiae cryo-FIB lamellae

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.638, 2.638)

Details:

The tilt series stacks (.st file) and rawtlt files (in EMPIAR_upload_nonCHX/Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the EMPIAR_upload_nonCHX/mdocs folder. Tilt series stacks are then aligned in IMOD.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

6. Reconstructed tomograms of vehicle-treated S. cerevisiae lamellae used for segmentation of mitochondria

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(682, 960)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(15.83, 15.83)

Details:

Bin6 tomograms are reconstructed from Warp after IMOD alignment. The coordinates of 80S ribosome and co-translating ribosome are provided in the EMPIAR_upload_nonCHX/Particle_lists folder.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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