EMPIAR-11465 - Cryo electron tomography dataset of purified human TREX-mRNPs [multiple data sets in TIFF and MRC formats]

EMPIAR-11465

Cryo electron tomography dataset of purified human TREX-mRNPs [multiple data sets in TIFF and MRC formats]

Publication:

mRNA recognition and packaging by the human transcription-export complex

Pacheco-Fiallos B, Vorländer MK, Riabov-Bassat D, Fin L, O'Reilly FJ, Ayala FI, Schellhaas U, Rappsilber J, Plaschka C

Nature 616 (2023) 828-835

PMID: 37020021

DOI: 10.1038/s41586-023-05904-0

Related EMDB entry:

EMD-16753

Deposited:

2023-02-21

Released:

2023-05-11

Last modified:

2023-05-11

Imageset size:

1.14 TB

Imageset DOI:

10.6019/EMPIAR-11465

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
tilt series
reconstructed volumes
subtomograms

Image Sets

1. Compressed movies of individual tilt exposures

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

6650

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.38, 1.38)

Details:

Unaligned movie frames of the individual tilt exposures. Each movie contains 6 frames and was exposed with 1.97 electrons per Å^2, or 0.3 electrons per Å^2 per frame. Movies are compressed and require the gainref file "CountRef_TS_TS_test_02_000_0.0.mrc" (uploaded in a separate directory) for motion correction. Each file has an .mdoc file associated that describes details of the exposure. These are found in the folder "mdoc_individual_tilts". In addition, the folder "tomostar" contains a .tomostar file for each tilt series that contains the information on tilt series alignment in Warp format (version 1.09). The folder "gainref" possesses the gain reference file to unpack and motion correct the tilt movie frames.

Files:

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2. Motion corrected tilt exposures

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

6650

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.38, 1.38)

Details:

Motion corrected individual tilt exposures

Files:

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)

3. Unbinned, unaligned tilt series as output by SerialEM.

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

117

Image size:

(5760, 4092)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.38, 1.38)

Details:

Each tilt series contains 61 tilt images, collected from -60 to +60 degrees in two degree increments, using the dose-symmetric Hagen scheme. The folder also contains SerialEM .log files with details about tilt series aquistion, and Serial .mdoc files with details about the tilt series.

Files:

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)

4. Reconstructed tomograms, binned to a pixel size of 10 Å/px

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

109

Image size:

(566, 786)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(10.0, 10.0)

Details:

Reconstructed tomograms, binned to a pixel size of 10 Å/px. Tomograms were reconstructed with Warp

Files:

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. Denoised, reconstructed tomograms, binned to a pixel size of 10 Å/px

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

109

Image size:

(566, 786)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(10.0, 10.0)

Details:

Denoised, reconstructed tomograms, binned to a pixel size of 10 Å/px. Tomograms were denoised using Noise2Map (part of the Warp package).

Files:

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. Extracted subtomograms that were used in the final reconstruction

Category:

subtomograms

Image format:

MRC

No. of images or tilt series:

1096

Image size:

(180, 180)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.0, 3.0)

Details:

Reconstructed subtomograms used for the final reconstruction, binned to 3Å/px al at bnox size of 180px. The folder also contains 3D ctf subvolumes for each subtomogram. The folder "star_file" contains a RELION (v3.1) star file that contains the refined orientations of each subtomogram.

Files:

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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