EMPIAR-10343 - CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a holey carbon grid (strongly preferred orientations) [multiple data sets in TIFF, MRC and MRCS formats]

EMPIAR-10343

CryoEM dataset containing multiple conformations of the asymmetric αVβ8 integrin bound to latent TGF-β on a holey carbon grid (strongly preferred orientations) [multiple data sets in TIFF, MRC and MRCS formats]

Publication:

Cryo-EM Reveals Integrin-Mediated TGF-β Activation without Release from Latent TGF-β

Campbell MG, Cormier A, Ito S, Seed RI, Bondesson AJ, Lou J, Marks JD, Baron J, Cheng Y, Nishimura SL

Cell (2020)

PMID: 31955848

DOI: 10.1016/j.cell.2019.12.030

Related EMDB entry:

EMD-20794 EMD-20800 EMD-20802 EMD-20798 EMD-20801 EMD-20797 EMD-20799 EMD-21125

Deposited:

2019-10-23

Released:

2020-01-31

Last modified:

2020-04-24

Imageset size:

1.25 TB

Imageset DOI:

10.6019/EMPIAR-10343

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - processed

Image Sets

1. Unaligned 80-frame movies of αVβ8 integrin bound to latent TGF-β on a holey carbon grid

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1684

Image size:

(7676, 7420)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.6725, 0.6725)

Details:

αVβ8 integrin bound to latent TGF-β on holey carbon grids (particles have strongly preferred orientations): 1684 unaligned uncorrected movies were recorded automatically using SerialEM on a K2 camera in super-resolution (dstep=2.5) mode on a Titan Krios microscope operated at 300 kV (Cs=2.7) equipped with an energy filter using a slit width of 20 eV. The 16 second movies contain 80 frames and the super resolution pixel size is 0.6725 Å/px. The total dose per movie is ~70 e/Å^2. The gain reference, a file containing coordinates for a single dead column, and a list of the 1364 micrographs that were used for downstream processing are included.

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2. Dose-weighted aligned micrographs of αVβ8 integrin bound to latent TGF-β on a holey carbon grid

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

1684

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.345, 1.345)

Details:

αVβ8 integrin bound to latent TGF-β on holey carbon grids (particles have strongly preferred orientations): 1684 aligned and dose-weighted (in MotionCor2) micrographs recorded automatically using SerialEM on a K2 camera (dstep=5) in super-resolution mode on a Titan Krios microscope operated at 300 kV (Cs=2.7) equipped with an energy filter using a slit width of 20 eV. Images were binned by 2 using Fourier cropping and the binned pixel size is 1.345. The total dose per micrograph is ~70 e/Å^2. A list of the 1364 micrographs that were used for downstream processing is included.

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. Dose-weighted aligned particle stacks of αVβ8 integrin bound to latent TGF-β on a holey carbon grid

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

68356

Image size:

(300, 300)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.345, 1.345)

Details:

αVβ8 integrin bound to latent TGF-β on holey carbon grids (particles have strongly preferred orientations): Stacks of 68,356 dose-weighted (in MotionCor2) particles contributing to the seven conformational snapshots described in the publication . Particles were selected after extensive 2D- and 3D classification. Images were recorded automatically using SerialEM on a K2 camera (dstep=5) in super-resolution mode on a Titan Krios microscope operated at 300 kV (Cs=2.7) equipped with an energy filter using a slit width of 20 eV. Images were binned by 2 using Fourier cropping and the binned pixel size is 1.345. This particle stack was combined with a stack of particles collected on graphene oxide to complement preferred orientations. The graphene oxide particle stack is deposited with the accession number EMPIAR-10344.

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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