EMPIAR-13358 - Cryo-EM structure of the Danio rerio tRNA ligase complex [multiple data sets in TIFF and MRCS formats]

EMPIAR-13358

Cryo-EM structure of the Danio rerio tRNA ligase complex [multiple data sets in TIFF and MRCS formats]

Publication:

Structural and biochemical characterization of the 3'-5' tRNA splicing ligases

Chamera S, Zajko W, Czarnocki-Cieciura M, Jaciuk M, Koziej Ł, Nowak J, Wycisk K, Sroka M, Chramiec-Głąbik A, Śmietański M, Gołębiowski F, Warmiński M, Jemielity J, Glatt S, Nowotny M

The Journal of biological chemistry 301 (2025)

PMID: 40220997

DOI: 10.1016/j.jbc.2025.108506

Related EMDB entry:

EMD-52744

Deposited:

2026-02-16

Released:

2026-03-16

Last modified:

2026-03-16

Imageset size:

3.73 TB

Imageset DOI:

10.6019/EMPIAR-13358

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame movies of Danio rerio tRNA ligase complex (truncated variant)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9942

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.84, 0.84)

Details:

Gain-corrected, unaligned multi-frame movies collected with Krios G3i microscope + K3 detector (superresolution mode, binned 2x with EPU) with 20 deg stage tilt. Voltage: 300 kV; spherical aberration: 2.7; dose per frame: 1 e/A^2 (total dose: 41.09 e/A^2 fractionated over 40 frames). Defocus range (nominal): -2.5, -2.0, -1.5, -0.9 µm. Objective aperture retracted, C2 aperture: 50 µm.

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2. Aligned particles of Danio rerio tRNA ligase complex (truncated variant)

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

179455

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.84, 0.84)

Details:

Aligned particles with corresponding Relion-3 STAR file. Micrographs were initially 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)

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Citations

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

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)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

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

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Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

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)