EMPIAR-12146 - Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex [7044 multi-frame micrographs composed of 50 frames each in TIFF format]

EMPIAR-12146

Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex [7044 multi-frame micrographs composed of 50 frames each in TIFF format]

Publication:

Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system

Feng Z, Yashiro Y, Tomita K

Nucleic acids research (2024)

PMID: 39228374

DOI: 10.1093/nar/gkae735

Related EMDB entry:

EMD-60564 EMD-60561 EMD-60563 EMD-60562

Deposited:

2024-06-20

Released:

2024-09-26

Last modified:

2024-09-26

Imageset size:

1.69 TB

Imageset DOI:

10.6019/EMPIAR-12146

Experimental metadata:

Download xml json

Deposited via PDBj

Contains:

micrographs - multiframe

Image Sets

1. Imageset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7044

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

- Microscope: FEI TITAN Krios
- Acceleration voltage (kV): 300
- Pixel size (Å/pix): 0.83
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (nm): -800 to -1800
- Detector: Gatan K3 BIOQUANTUM
- Average electron dose per image (e-/A2): 50
- Number of frames per image: 50
- Please use gain.mrc as a gain reference.
- In CryoSPARC, select "flip gain ref in Y".

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)

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)

EMICSS: added-value annotations for EMDB entries.

Duraisamy AK, Fonseca N, Kleywegt GJ, Patwardhan A, Morris KL. (2025)

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification

Williams HM, Curtis WA, Haubner M, Hruby J, Drabbels M, Lorenz UJ. (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)

See all citations

Protein Data Bank Japan News

[2025-10-01]

301 new PDB entries have been released on 2025-10-01.

[2025-09-26]

[wwPDB] Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report

[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

See all news