EMPIAR-12904 - CryoEM dataset of M. mazei topoisomerase VI-minicircle DNA complex [50906 multi-frame micrographs composed of 0 frames each in EER format]

EMPIAR-12904

CryoEM dataset of M. mazei topoisomerase VI-minicircle DNA complex [50906 multi-frame micrographs composed of 0 frames each in EER format]

Publication:

Mechanisms of supercoiled DNA recognition and DNA cleavage control in Top6, a homolog of Spo11 and TOPRIM-based bacterial immunity nucleases

Richman DE, Wendorff TJ, Rashid F, Beck C, Johnson HR, Eckerty RA, Fogg JM, Baker ML, Zechiedrich L, Berger JM

(---)

Related EMDB entry:

EMD-70239 EMD-70259 EMD-70232

Deposited:

2025-07-30

Released:

2026-03-02

Last modified:

2026-03-02

Imageset size:

29.64 TB

Imageset DOI:

10.6019/EMPIAR-12904

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned eer micrographs of WT M mazei Top6-327 bp minicircle DNA-ADPNP complex

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

50906

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.959, 0.959)

Details:

~80% of this dataset was collected at 30 degree stage tilt (n23feb, may, jun, jul folders). The n23jan folder was collected at 0 degree tilt. Data were collected at National Center for CryoEM Access and Training (New York Structural Biology Center) on Krios 7 "Matthew", camera: TFS Falcon IV, image shift at 130kx mag, exposure settings: 7.0 s [images saved in eer format], e flux: ~6 e-/px/s with ~50 e-/Å total dose, pixel size: ~0.959Å/px (nominal) [0.926Å(calibrated against apoF)] (e- counting with an image dimension of 4096x4096 px), energy filter: Selectris 10-20 eV, defocus range: -0.8 µm to -2.5 µm (nominal).

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)

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

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)

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

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

Ultrathin liquid cells for microsecond time-resolved cryo-EM.

Curtis WA, Wenz J, Krüger CR, Barrass SV, Drabbels M, Lorenz UJ. (2026)

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

Species-specific structural adaptation of the potyviral coat protein in virions and virus-like particles.

Koritnik N, Kežar A, Kavčič L, Žnidarič MT, Leonardi A, De S, Pollari M, Mäkinen K, Podobnik M. (2026)

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

See all citations

Protein Data Bank Japan News

[2026-03-06]

[wwPDB] PDB Reaches a New Milestone

[2026-03-04]

362 new PDB entries have been released on 2026-03-04.

[2026-02-11]

[wwPDB] New PDB Beta Archive Available for Testing

[2026-01-20]

[wwPDB] EMDB Surpasses 10,000 Entries in a Year

[2026-01-13]

[wwPDB] wwPDB Shared Responsibilities on Data Processing

[2026-01-08]

[wwPDB] Time-stamped Copies of PDB and EMDB Archives

[2025-12-17]

[wwPDB] 20,000 Structures Deposited to the PDB in 2025

[2025-12-04]

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

[2025-11-19]

[wwPDB] Coming soon: wwPDB Data Processing Distribution Changes

[2025-10-30]

[wwPDB] Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

See all news