EMPIAR-13055 - Cryo-electron tomography of the MTEC transition zone [multiple data sets in MRC format]

EMPIAR-13055

Cryo-electron tomography of the MTEC transition zone [multiple data sets in MRC format]

Publication:

The luminal ring protein C2CD3 acts as a radial in-to-out organizer of the distal centriole and appendages

Bertiaux E, Louvel V, McCafferty CL, van den Hoek H, Batman U, Mukherjee S, Bournonville L, Mercey O, Méan I, Righetto RD, Müller A, Van der Stappen P, Buss G, Daraspe J, Genoud C, Stearns T, Engel BD, Hamel V, Guichard P

PLoS biology 23 (2025)

PMID: 41364719

DOI: 10.1371/journal.pbio.3003519

Related EMDB entry:

EMD-55386

Deposited:

2025-10-15

Released:

2025-11-13

Last modified:

2026-01-20

Imageset size:

1.07 TB

Imageset DOI:

10.6019/EMPIAR-13055

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
tilt series

Image Sets

1. IsoNet tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

SIGNED BYTE

Pixel spacing:

(14.08, 14.08)

Details:

Tomograms were denoised using IsoNet after running cryo-CARE. One model per tomogram was trained.

Files:

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2. cryo-CARE tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

SIGNED BYTE

Pixel spacing:

(14.08, 14.08)

Details:

Tomograms were denoised using cryo-CARE. One model per tomogram was trained.

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. CTF-corrected tomograms (phase-flipped)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(14.08, 14.08)

Details:

Tomograms reconstructed with CTF correction by phase-flipping in IMOD.

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 tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(14.08, 14.08)

Details:

Raw tomograms reconstructed by filtered backprojection in IMOD.

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. Tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 3712)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.52, 3.52)

Details:

Tilt series processed with Etomo in IMOD. Bad tilts were manually excluded. Corresponding .xf and .tlt files are available for the tomogram reconstruction, as well as the original TS before dose-filtering and the stacks generated from ODD/EVEN raw frames from cryo-CARE denoising.

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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Citations

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)