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

Related EMDB entry:
Deposited:
2023-02-21
Released:
2023-05-11
Last modified:
2023-05-11
Imageset size:
1.14 TB
Imageset DOI:
Experimental metadata:
Download xml json
Contains:
  • micrographs - multiframe
  • micrographs - single frame
  • tilt series
  • reconstructed volumes
  • subtomograms
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:
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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.
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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:
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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).
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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.
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