EMPIAR-13511 - 33,592 raw cryo-EM images of B. megaterium gas vesicles at 1.518 A per pixel [multiple data sets in EER, MRC and JPEG formats]

EMPIAR-13511

33,592 raw cryo-EM images of B. megaterium gas vesicles at 1.518 A per pixel [multiple data sets in EER, MRC and JPEG formats]

Publication:

Cryo-EM structure of gas vesicles for buoyancy-controlled motility

Huber ST, Terwiel D, Evers WH, Maresca D, Jakobi AJ

Cell 186 (2023) 975-986.e13

PMID: 36868215

DOI: 10.1016/j.cell.2023.01.041

Related EMDB entry:

EMD-14238

Deposited:

2026-04-01

Released:

2026-05-05

Last modified:

2026-05-05

Imageset size:

16.72 TB

Imageset DOI:

10.6019/EMPIAR-13511

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. 33592 unaligned multi-frame EER movies of B. megaterium gas vesicles at 1.518 A per pixel

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

33592

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.518, 1.518)

Details:

33,592 movies collected on a Titan Krios G4 (Thermo Fisher Scientific) with a C-FEG source, using a Falcon4i detector in EER format. Acquired at EMBL Heidelberg on 29 July 2022 with the help of Wim Hagen.
Pixel size: 1.518 Å
EER fractions per movie: 1,971
Defocus range: 0.25 to 0.75 µm
Total exposure: 10 e⁻/Å²
# Notes
This dataset covers the same grids and sample as described in Huber et al. (2023) Cell, but was acquired at a larger scale, newer microscope and coarser pixel size than the dataset used in that publication. The goal was to increase the amount of gas vesicles imaged to reconstruct the central seam. However, because of the large variation in diameter, even a dataset of this size did not provide an adequate amount of same-diameter gas vesicles for proper averaging. Subsequent samples were pressure-treated for homogenization (only small GVs survive), and led to much more useful data.
This dataset however was used by Flip Jansen in his Master's thesis, which investigated the overall morphology of B. megaterium gas vesicles through image analysis:
Jansen (2023), "A Pipeline for Segmentation and Structural Feature Extraction in Cryo-EM Single Particle Analysis of Gas Vesicles"
https://resolver.tudelft.nl/uuid:1a9ca4cd-f4d8-4f2f-bac1-f0bd396232c6

Files:

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2. Aligned movies of B. megaterium gas vesicles at 1.518 A per pixel

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

33592

Image size:

(4096, 4096)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(1.518, 1.518)

Details:

EER micrographs, aligned with RELION 4, saved as 16 bit MRC.

Files:

This entry cannot be downloaded from PDBj.

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3. Thumbnails of aligned movies of B. megaterium gas vesicles at 1.518 A per pixel

Category:

micrographs - single frame

Image format:

JPEG

No. of images or tilt series:

33592

Image size:

(4096, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

JPEG thumbnails of aligned micrographs

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.

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