EMPIAR-12457 - Cryo-ET dataset of FIB-milled mock infected (control) human monocyte-derived macrophages [multiple data sets in MRC format]

EMPIAR-12457

Cryo-ET dataset of FIB-milled mock infected (control) human monocyte-derived macrophages [multiple data sets in MRC format]

Publication:

Passage of the HIV capsid cracks the nuclear pore

Kreysing JP, Heidari M, Zila V, Cruz-Leon S, Obarska-Kosinska A, Laketa V, Rohleder L, Welsch S, Köfinger J, Turoňová B, Hummer G, Kräuslich HG, Beck M

Cell (2025)

DOI: 10.1016/j.cell.2024.12.008

Related EMDB entry:

EMD-52138 EMD-52142 EMD-52141 EMD-52143 EMD-52139 EMD-52140 EMD-52144

Deposited:

2024-11-19

Released:

2025-01-20

Last modified:

2025-01-20

Imageset size:

324.55 GB

Imageset DOI:

10.6019/EMPIAR-12457

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. Raw tilt-series of human macrophage cells

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(2.414, 2.414)

Details:

Each tilt series stack is ordered from lowest to highest tilt angle and contains already aligned tilt images (10 frames each aligned with alignframes on the fly in SerialEM). The mdoc metadata files are also provided.

Files:

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2. Tilt cleaned, dose-filtered tilt-series of human macrophage cells

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.414, 2.414)

Details:

Tilt cleaned (see TS_cleaning_MDM-inf.csv file) and dose-filtered tilt series. These stacks were used for tomogram reconstruction in IMOD and novaCTF. The relevant alignment files (.xf and .tlt) are provided in the alignment_files folder

Files:

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Download a list of selected files.

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3. Reconstructed tomograms of human macrophage cells (4x binning and filtered with sirt-like filter)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 1024)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(9.656, 9.656)

Details:

Tomograms were reconstructed in IMOD with 4x binning and a sirt-like filter for better visualization. All tomograms have a z-height of 450 px (at 4x binning).

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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Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

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