EMPIAR-12570 - Cryo electron micrographs of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA [multiple data sets in TIFF and MRCS formats]

EMPIAR-12570

Cryo electron micrographs of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA [multiple data sets in TIFF and MRCS formats]

Publication:

Structural and functional interrelationships of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis

Wang Y

(---)

DOI: 10.1016/j.str.2025.04.015

Related EMDB entry:

EMD-62041 EMD-62042

Deposited:

2025-02-14

Released:

2026-07-07

Last modified:

2026-07-07

Imageset size:

2.21 TB

Imageset DOI:

10.6019/EMPIAR-12570

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - unprocessed

Image Sets

1. Cryo electron micrographs of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2695

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.072, 1.072)

Details:

These micrographs doesn't need a gain file.

Files:

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2. Particles for cryo electron micrographs of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

1429

Image size:

(256, 256)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(1.072, 1.072)

Details:

The folder cryosparc/J1 is "Imported particles" of CryoSPARC-v4.3.1, and the particles is imported from "Particle extraction" of relion-v3.1.3.
The folder cryosparc/J18 is "Homogeneous Refinement" of CryoSPARC-v4.3.1, and this "Homogeneous Refinement" which imposed C1 symmetry is at a resolution of 3.12 angstrom.
The folder cryosparc/J26 is "Homogeneous Refinement" of CryoSPARC-v4.3.1, and this "Homogeneous Refinement" which imposed C2 symmetry is at a resolution of 2.87 angstrom.

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

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

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Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

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.

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Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (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)

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

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

See all citations

Protein Data Bank Japan News

[2026-07-08]

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