EMPIAR-12976 - Cryo-EM SPA dataset of the human nucleosome with the H2AX variant [multiple data sets in EER format]

EMPIAR-12976

Cryo-EM SPA dataset of the human nucleosome with the H2AX variant [multiple data sets in EER format]

Publication:

Structural insights into γH2Ax containing nucleosomes

Panigrahi R, Edwards R, Islam MT, Lu J, Kulepa A, Kim TH, Mark Glover JN

Nucleic acids research 53 (2025)

PMID: 41123210

DOI: 10.1093/nar/gkaf1028

Related EMDB entry:

EMD-48394 EMD-48403 EMD-48392 EMD-48395 EMD-48396

Deposited:

2025-09-11

Released:

2025-10-30

Last modified:

2025-10-30

Imageset size:

5.66 TB

Imageset DOI:

10.6019/EMPIAR-12976

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned multi-frame micrographs of H2AX containing nucleosome

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

4800

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.77, 0.77)

Details:

Raw movies total exposure does 50 e/A^2

Files:

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2. Unaligned multi-frame micrographs of H2AX containing nucleosome

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

618

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.77, 0.77)

Details:

Raw movies total exposure does 50 e/A^2 collected at a tilt angle of 17 degrees

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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3. Unaligned multi-frame micrographs of H2AX containing nucleosome

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

3068

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.77, 0.77)

Details:

Raw movies total exposure does 50 e/A^2 collected at a tilt angle of 35 degrees

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.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

4. Unaligned multi-frame micrographs of H2AX containing nucleosome

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

1349

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.77, 0.77)

Details:

Raw movies total exposure does 50 e/A^2 collected at a tilt angle of 35 degrees

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

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Ramírez-Aportela E, Zarrabeitia OL, Fonseca YC, Ceska T, Subramaniam S, Carazo JM, Sorzano COS. (2026)

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)

Helical reconstruction of amyloids in cryoSPARC.

Schaefer JH, O'Neill RT, Donnelly JP, Powers ET, Kelly JW, Lander GC. (2026)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (2026)

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

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

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

He L, Bartesaghi A. (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)

Unbend, correction of local beam-induced sample motion in cryo-EM images using a 3D spline model.

Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

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)

See all citations

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