EMPIAR-12405 - Gelsolin-severed and capped F-actin raw data from 'Mechanism of actin filament severing and capping by gelsolin' [multiple data sets in TIFF format]

EMPIAR-12405

Gelsolin-severed and capped F-actin raw data from 'Mechanism of actin filament severing and capping by gelsolin' [multiple data sets in TIFF format]

Publication:

Mechanism of actin filament severing and capping by gelsolin

Barrie KR, Rebowski G, Dominguez R

Nature structural & molecular biology (2024)

PMID: 39448849

DOI: 10.1038/s41594-024-01412-5

Related EMDB entry:

EMD-43268 EMD-43264 EMD-43316 EMD-43274 EMD-43262 EMD-43263

Deposited:

2024-06-13

Released:

2024-12-09

Last modified:

2024-12-09

Imageset size:

13.26 TB

Imageset DOI:

10.6019/EMPIAR-12405

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Dataset 1

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2945

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

Dataset 1. Super-resolution movies (binned 2x during motion correction). Total dose = 45.6 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_02222023/gainref.

Files:

This entry cannot be downloaded from PDBj.

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 2

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

6806

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

Dataset 2. Super-resolution movies (binned 2x during motion correction). Total dose = 43.7 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_03092023/gainref.

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.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

3. Dataset 3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3682

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

Dataset 3. Super-resolution movies (binned 2x during motion correction). Total dose = 43.7 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_04112023/gainref.

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.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

4. Dataset 4

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5963

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

Dataset 4. Super-resolution movies (binned 2x during motion correction). Total dose = 43.7 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_04122023/gainref.

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.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

5. Dataset 5

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7814

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

Dataset 5. Super-resolution movies (binned 2x during motion correction). Total dose = 44 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_07022023/gainref.

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.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

6. Mg-F-actin Severed Dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4594

Image size:

(8184, 11520)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.54, 0.54)

Details:

PLEASE NOTE: This dataset was not used to generate the associated EMDs and PDBs. This dataset was collected under different sample preparations conditions (Mg-F-actin instead of Ca-G-actin) to demonstrate F-actin severing by gelsolin. The grids used for this dataset were also different (2nm ultra-thin carbon), resulting in a minor orientation bias. Please see methods and Extended Data Fig. 4 in the publication (doi.org/10.1038/s41594-024-01412-5) for more details.

Super-resolution movies (binned 2x during motion correction). Total dose = 45.3 electrons/Å^2. The gain reference is also provided as a .mrc file in data/Beckman_04052024/gainref.

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.

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

[2024-12-25]

203 new PDB entries have been released on 2024-12-25.

[2024-11-28]

[wwPDB] Access SDF/MOL formatted CCD files from the PDB archive

[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