EMPIAR-11722 - Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP [multiple data sets in TIFF format]

EMPIAR-11722

Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP [multiple data sets in TIFF format]

Publication:

An unusual conformation from Na + -sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na + -binding.

Abe K, Nishizawa T, Artigas P

Biochimica Biophysica Acta Molecular Cell Research 1870 (2023)

PMID: 37482134

DOI: 10.1016/j.bbamcr.2023.119543

Related EMDB entry:

EMD-35488 EMD-35489 EMD-35491

Deposited:

2023-10-11

Released:

2024-08-23

Last modified:

2024-08-23

Imageset size:

1.88 TB

Imageset DOI:

10.6019/EMPIAR-11722

Experimental metadata:

Download xml json

Deposited via PDBj

Contains:

micrographs - multiframe

Image Sets

1. K3 movies for non gastric proton pump WT with Na, AlF and ADP

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1723

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

- Please use 'movie_gain_ref_estimate.mrc' as a gain reference without rotation or flipping in RELION.
- The gain reference (movie_gain_ref_estimate.mrc) was generated with relion_estimate_gain by averaging many frames.
- The flux is 1.06 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 3x3 image shift but grouping was not applied during processing.

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 non gastric proton pump K794A mutant in NaE1AMPPCP state

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3204

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

- Please use 'CountRef_abe1-3_11-001_0000_Sep09_09.26.25.mrc' as a gain reference without rotation or flipping in RELION.
- The flux is 1.06 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 3x3 image shift but grouping was not applied during processing.

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 non gastric proton pump K794S mutant in NaE1AMPPCP state

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2187

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

- Please use 'CountRef_abe2-1_22-001_0000_Sep10_01.28.37.mrc' as a gain reference without rotation or flipping in RELION.
- The flux is 1.06 e/A2/frame.
- Cs is 2.7 mm.
- Four digits in the file name represent image shift directions.
- Movies were recorded with 3x3 image shift but grouping was not applied during processing.

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)

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

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

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)

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)

Cryo-EM Structure Reconstruction by Gaussian Splatting: Pushing the Resolution to Extreme

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2025)

Molecular exaptation by the integrin αI domain.

Hollis JA, Chan MC, Malik HS, Campbell MG. (2025)

See all citations

Protein Data Bank Japan News

[2025-09-17]

231 new PDB entries have been released on 2025-09-17.

[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