EMPIAR-11125 - Cryo electron tomography of H. neapolitanus alpha-carboxysomes [multiple data sets in MRC format]

EMPIAR-11125

Cryo electron tomography of H. neapolitanus alpha-carboxysomes [multiple data sets in MRC format]

Publication:

Rubisco forms a lattice inside alpha-carboxysomes

Metskas LA, Ortega D, Oltrogge LM, Blikstad C, Laughlin T, Savage DF, Jensen GJ

bioRxiv (2022)

DOI: 10.1101/2022.01.24.477598

Related EMDB entry:

EMD-27654

Deposited:

2022-07-18

Released:

2022-08-12

Last modified:

2022-09-05

Imageset size:

483.42 GB

Imageset DOI:

10.6019/EMPIAR-11125

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
picked particles - multiframe - unprocessed

Image Sets

1. Reconstructed sample tomograms of purified alpha-carboxysomes, plus frames

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(511, 313)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.832, 8.832)

Details:

SIRT-like filtered reconstructed tomograms with bin8 pixel size. These tomograms illustrate different features of alpha-carboxysomes, noted in the accompanying citation. Tomograms have different image heights; see MRC header for more details. Frame stacks (gain-corrected) and mdoc files are included for users wishing to reconstruct in their own programs.

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. Reconstructed sample tomograms of wild-type H. neapolitanus cells, plus frames

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 500)

Pixel type:

SIGNED BYTE

Pixel spacing:

(8.612, 8.612)

Details:

SIRT-reconstructed tomograms with bin4 pixel size. These tomograms illustrate different features of alpha-carboxysomes in vivo, noted in the accompanying citation. Tomograms have different image heights; see MRC header for more details. Frame stacks and mdoc files are included for users wishing to reconstruct in their own programs.

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. Complete set of subtomograms for Rubisco subtomogram average

Category:

picked particles - multiframe - unprocessed

Image format:

MRC

No. of images or tilt series:

32930

Image size:

(160, 160)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.104, 1.104)

Details:

subtomograms.tar.gz contains the complete set of Rubisco subtomograms from the purified alpha-carboxysome dataset. The file pattern is subtomograms/particle_*.mrc, and the picked particles file is subtomograms/particles.csv. Subtomograms were cropped in Dynamo from from bin1 WBP tomograms reconstructed in novaCTF. The particles.csv text file contains position and orientation information for each subtomogram, as well as defocus, carboxysome number, cross-correlation coefficient, and other data to allow users to import subtomograms into the software package of their choice. A detailed description of the csv information is in the csvColumnDefinitions.txt file, also in the subtomograms directory.

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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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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