EMPIAR-11450 - Cryo electron tomography of Cytochalasin D-induced protrusions of Drosophila S2 cells - Datasets 1 - 4 [multiple data sets in TIFF and MRC formats]

EMPIAR-11450

Cryo electron tomography of Cytochalasin D-induced protrusions of Drosophila S2 cells - Datasets 1 - 4 [multiple data sets in TIFF and MRC formats]

Publication:

CryoET shows cofilactin filaments inside the microtubule lumen

Ventura Santos C, Rogers SL, Carter AP

bioRxiv (2023)

DOI: 10.1101/2023.03.31.535077

Related EMDB entry:

EMD-16693 EMD-16685

Deposited:

2023-02-10

Released:

2023-07-10

Last modified:

2023-07-10

Imageset size:

478.88 GB

Imageset DOI:

10.6019/EMPIAR-11450

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
reconstructed volumes

Image Sets

1. Dataset 1: Raw multi-frame tilt images of Cytochalasin D induced protrusions of Drosophila S2 cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.952, 2.952)

Details:

Data from Dataset 1. Raw multi-frame movies of tilt series collected on protrusions of Drosophila S2 cells induced with 2.5 uM Cytochalasin D for 4 hours. The gain reference and defects files are provided within the folder. The pixel size is 2.952 Å/pixel. Data was collected on a K2 summit. Metadata from tilt series acquisition (Mdoc files) is provided inside the Mdoc folder.

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. Dataset 1: Binned, deconvolved tomograms of induced Drosophila S2 cell protrusions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1124, 1124)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(11.808, 11.808)

Details:

Dataset 1: Tomograms binned by 4 (11.808 Å/pixel), reconstructed and deconvolved in WARP.

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. Dataset 2: Raw multi-frame tilt images of Cytochalasin D induced protrusions of Drosophila S2 cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.952, 2.952)

Details:

Data from Dataset 2. Raw multi-frame movies of tilt series collected on protrusions of Drosophila S2 cells induced with 2.5 uM Cytochalasin D for 4 hours. The gain reference and defects files are provided within the folder. The pixel size is 2.952 Å/pixel. Data was collected on a K2 summit. Metadata from tilt series acquisition (Mdoc files) is provided inside the Mdoc folder.

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. Dataset 2: Binned, deconvolved tomograms of induced Drosophila S2 cell protrusions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(960, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(11.808, 11.808)

Details:

Dataset 2: Tomograms binned by 4 (11.808 Å/pixel), reconstructed and deconvolved in WARP.

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. Dataset 3: Raw multi-frame tilt images of Cytochalasin D induced protrusions of Drosophila S2 cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.952, 2.952)

Details:

Data from Dataset 3. Raw multi-frame movies of tilt series collected on protrusions of Drosophila S2 cells induced with 2.5 uM Cytochalasin D for 4 hours. The gain reference and defects files are provided within the folder. The pixel size is 2.952 Å/pixel. Data was collected on a K2 summit. Metadata from tilt series acquisition (Mdoc files) is provided inside the Mdoc folder.

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)

6. Dataset 3: Binned, deconvolved tomograms of induced Drosophila S2 cell protrusions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(960, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(11.808, 11.808)

Details:

Dataset 3: Tomograms binned by 4 (11.808 Å/pixel), reconstructed and deconvolved in WARP.

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)

7. Dataset 4: Raw multi-frame tilt images of Cytochalasin D induced protrusions of Drosophila S2 cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.952, 2.952)

Details:

Data from Dataset 4. Raw multi-frame movies of tilt series collected on protrusions of Drosophila S2 cells induced with 5 uM Cytochalasin D for 4 hours. The gain reference and defects files are provided within the folder. The pixel size is 2.952 Å/pixel. Data was collected on a K2 summit. Metadata from tilt series acquisition (Mdoc files) is provided inside the Mdoc folder.

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)

8. Dataset 4: Binned, deconvolved tomograms of induced Drosophila S2 cell protrusions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(960, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(11.808, 11.808)

Details:

Dataset 4: Tomograms binned by 4 (11.808 Å/pixel), reconstructed and deconvolved in WARP.

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

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

Laser flash melting cryo-EM samples to overcome preferred orientation.

Straub MS, Harder OF, Mowry NJ, Barrass SV, Hruby J, Drabbels M, Lorenz UJ. (2025)

In situ structure determination of conformationally flexible targets using nextPYP.

Liu HF, Zhou Y, Huang Q, Martin J, Bartesaghi A. (2025)

CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles.

Zhang H, Zheng D, Wu Q, Yan N, Peng H, Hu Q, Peng Y, Yan Z, Shi Z, Bao C, Hu M. (2025)

Few-shot learning for non-vitrified ice segmentation.

Vivas-Lago A, Castaño-Díez D. (2025)

Automated removal of corrupted tilts in cryo-electron tomography.

Majtner T, Turoňová B. (2025)

Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.

Van CTS, Reboul CF, Caesar JJE, Meana-Pañeda R, Lountos GT, Deme JC, Bryant OJ, Johnson S, Piczak CT, Valkov E, Lea SM, Elmlund H. (2025)

Reanalysis of cryo-EM data reveals ALK-cytokine assemblies with both 2:1 and 2:2 stoichiometries.

Felix J, De Munck S, Bazan JF, Savvides SN. (2025)

See all citations

Protein Data Bank Japan News

[2025-09-24]

278 new PDB entries have been released on 2025-09-24.

[2025-07-17]

[wwPDB] Transitioning to PDBx/mmCIF and Extended PDB IDs

[2025-06-25]

[wwPDB] Extension to EMDB Accession Codes

[2025-04-18]

[wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

[2025-03-25]

Announcement of the PDBj Newsletter Vol.25 release

[2025-03-11]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2025-03-10]

[wwPDB] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models

[2025-01-30]

[wwPDB] Take the PDBx/mmCIF User Guide Survey and Win!

[2025-01-17]

[wwPDB] PDB-Dev now PDB-IHM

[2025-01-09]

[wwPDB] Time-stamped Copies of PDB and EMDB Archives

See all news