EMPIAR-12568 - Cryo electron micrographs of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2 [multiple data sets in TIFF and MRCS formats]

EMPIAR-12568

Cryo electron micrographs of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2 [multiple data sets in TIFF and MRCS formats]

Publication:

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

Wang Y, Wu J, Yang S, Li X, Wang J, Lv Q, Zhu X, Lu G, Zhang J, Shen W, Liu B, Lin J, Dong A

bioRxiv (2024)

DOI: 10.1101/2024.12.03.626673

Related EMDB entry:

EMD-62037 EMD-62038

Deposited:

2025-02-14

Released:

2025-07-25

Last modified:

2025-07-25

Imageset size:

1.33 TB

Imageset DOI:

10.6019/EMPIAR-12568

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - unprocessed

Image Sets

1. Cryo electron micrographs of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1521

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.072, 1.072)

Details:

These micrographs doesn't need a gain file.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

ダウンロードするファイル数やサイズによっては、膨大な時間がかかります。また、この機能は不安定で正常に動作しない可能性があり、ダウンロードされたファイルのチェックサムは検証されません。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

2. Particles for cryo electron micrographs of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

1497

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 3.05 angstrom.
The folder cryosparc/J22 is "Homogeneous Refinement" of CryoSPARC-v4.3.1, and this "Homogeneous Refinement" which imposed C2 symmetry is at a resolution of 2.81 angstrom.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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)

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)

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)

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)

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)

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

[2026-06-10]

333件のPDBエントリーが新たに公開されました。（2026-06-10付）