EMPIAR-11747 - In situ cryo-electron tomography of the T. pseudonana diatom PyShell [multiple data sets in MRC and TIFF formats]

EMPIAR-11747

In situ cryo-electron tomography of the T. pseudonana diatom PyShell [multiple data sets in MRC and TIFF formats]

Publication:

Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation

Shimakawa G, Demulder M, Flori S, Kawamoto A, Tsuji Y, Nawaly H, Tanaka A, Tohda R, Ota T, Matsui H, Morishima N, Okubo R, Wietrzynski W, Lamm L, Righetto RD, Uwizeye C, Gallet B, Jouneau PH, Gerle C, Kurisu G, Finazzi G, Engel BD, Matsuda Y

(---)

DOI: 10.1016/j.cell.2024.09.013

Related EMDB entry:

EMD-18709

Deposited:

2023-10-20

Released:

2024-10-08

Last modified:

2024-10-08

Imageset size:

81.81 GB

Imageset DOI:

10.6019/EMPIAR-11747

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
tilt series
micrographs - multiframe

Image Sets

1. Denoised bin4 tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.572, 8.572)

Details:

Tomograms denoised using cryo-CARE trained on each individual tomogram reconstructed from odd/even frames.

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. IMOD bin4 tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.572, 8.572)

Details:

IMOD reconstruction at bin4 using weighted backprojection without CTF correction. IMOD reconstruction files (.xf and .tlt) are provided in the imod_files/ 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)

3. Tilt series assembled from motion-corrected and averaged frames

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.143, 2.143)

Details:

Frames aligned with MotionCor2
Note: Frames per image varies

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. Raw frames

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

327

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.071, 1.071)

Details:

Movies acquired with a K3 detector in super-resolution mode using SerialEM. Gain reference and defects file are provided in the gainref/ directory. Metadata from the acquisition can be found in the mdocs/ 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)

Browse All Files

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

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)

See all citations

Protein Data Bank Japan News

[2024-11-20]

224 new PDB entries have been released on 2024-11-20.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024