EMPIAR-11723 - Cryo-EM structure of the gastric proton pump [multiple data sets in TIFF format]

EMPIAR-11723

Cryo-EM structure of the gastric proton pump [multiple data sets in TIFF format]

Publication:

Deep learning driven de novo drug design based on gastric proton pump structures.

Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A

Communications Biology 6 (2023)

PMID: 37726448

DOI: 10.1038/s42003-023-05334-8

Related EMDB entry:

EMD-35502 EMD-36424 EMD-35500 EMD-35501

Deposited:

2023-10-11

Released:

2024-11-08

Last modified:

2024-11-08

Imageset size:

7.34 TB

Imageset DOI:

10.6019/EMPIAR-11723

Experimental metadata:

Download xml json

Deposited via PDBj

Contains:

micrographs - multiframe

Image Sets

1. K3 movies for gastric proton pump with DQ-02

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9650

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.753, 0.753)

Details:

- Please use 'CountCDSRef_2022-11-24_14.24.17_220830B06_51-1_0000.mrc' as a gain reference without rotation or flipping in RELION.
- The flux is 1 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 5x5 image shift with two shots per hole.
- The pixel size in the image header is not correct.

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. K3 movies for gastric proton pump with DQ-06

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

8100

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.58, 0.58)

Details:

- Please use
'CountCDSRef_2022-10-21_12.30.19_220830C12_76-3_0000.mrc' for 'Movies' and
'CountCDSRef_2022-10-21_22.12.15_220830C12_82-17_0000.mrc' for 'Movies2'
as a gain reference without rotation or flipping in RELION.
- The flux is 1 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 5x5 image shift with two shots per hole.
- The pixel size in the image header is not correct.

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. K3 movies for gastric proton pump with DQ-18

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9200

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.753, 0.753)

Details:

- Please use 'CountCDSRef_2022-12-20_13.53.39_221213A02_67-1_0000.mrc' as a gain reference without rotation or flipping in RELION.
- The flux is 1 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 5x5 image shift with two shots per hole.
- The pixel size in the image header is not correct.

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. K3 movies for gastric proton pump with DQ-21

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7844

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.753, 0.753)

Details:

- Please use 'CountCDSRef_2023-04-27_15.38.01_230418C11_66-1_0000.mrc' as a gain reference without rotation or flipping in RELION.
- The flux is 1 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 5x5 image shift with two shots per hole.
- The pixel size in the image header is not correct.

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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He L, Bartesaghi A. (2026)

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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)

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

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

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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)