EMPIAR-12444 - Single particle reconstruction of E. coli TnsB in complex with right end fragment of Tn7 transposon [multiple data sets in TIFF and MRCS formats]

EMPIAR-12444

Single particle reconstruction of E. coli TnsB in complex with right end fragment of Tn7 transposon [multiple data sets in TIFF and MRCS formats]

Publication:

Structural basis of transposon end recognition explains central features of Tn7 transposition systems

Kaczmarska Z, Czarnocki-Cieciura M, Górecka-Minakowska KM, Wingo RJ, Jackiewicz J, Zajko W, Poznański JT, Rawski M, Grant T, Peters JE, Nowotny M

Molecular cell 82 (2022) 2618-2632.e7

PMID: 35654042

DOI: 10.1016/j.molcel.2022.05.005

Related EMDB entry:

EMD-13439 EMD-13440

Deposited:

2024-11-02

Released:

2025-02-03

Last modified:

2025-02-03

Imageset size:

4.12 TB

Imageset DOI:

10.6019/EMPIAR-12444

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame movies of E. coli TnsB in complex with right end fragment of Tn7 transposon

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

6692

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.86, 0.86)

Details:

Gain-corrected, unaligned multi-frame movies collected with Krios G3i microscope + K3 detector (superresolution mode, binned 2x with EPU). Voltage: 300 kV; spherical aberration: 2.7; dose per frame: 1 e/A^2 (total dose: 40.16 e/A^2 fractionated over 40 frames). Defocus range (nominal): -2.0, -1.7, -1.4, -1.1, -0.8, -0.5 µm. Objective aperture retracted, C2 aperture: 50 µm.

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. Aligned particles of E. coli TnsB in complex with right end fragment of Tn7 transposon (helical reconstruction)

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

450748

Image size:

(512, 512)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.86, 0.86)

Details:

Aligned particles with corresponding Relion-3 STAR file for helical reconstruction. Coordinates correspond to micrographs binned 2x during Motion correction.

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. Aligned particles of E. coli TnsB in complex with right end fragment of Tn7 transposon (single particle reconstruction)

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

901496

Image size:

(512, 512)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.86, 0.86)

Details:

Aligned particles with corresponding Relion-3 STAR file for single particle reconstruction. Particles were signal-subtracted; coordinates correspond to micrographs binned 2x during Motion correction.

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

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