EMPIAR-12329 - RNAP-TopoI complex on duplex scaffold [multiple data sets in TIFF and MRC formats]

EMPIAR-12329

RNAP-TopoI complex on duplex scaffold [multiple data sets in TIFF and MRC formats]

Publication:

DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli

Vidmar VV, Borde CB, Bruno LB, Takacs MT, Batisse CB, Saint-Andre CSA, Zhu CZ, Espeli OE, Lamour VL, Weixlbaumer AW

(---)

Related EMDB entry:

EMD-51267 EMD-51259 EMD-51256 EMD-51255 EMD-51253 EMD-51252 EMD-51254 EMD-51258 EMD-51257 EMD-51266

Deposited:

2024-10-03

Released:

2025-12-08

Last modified:

2025-12-08

Imageset size:

10.20 TB

Imageset DOI:

10.6019/EMPIAR-12329

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. unaligned multi-frame movies of RNAP-TopoI on duplex scaffold

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

21561

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.839, 0.839)

Details:

300 kV, Cs 2.7 mm, defocus range -0.8 – -2.5 um, total dose 56.60 e/A2
Movie frames are gain-corrected.

Files:

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2. all good particles of RNAP-TopoI on duplex scaffold

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

16044

Image size:

(360, 360)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.839, 0.839)

Details:

Particles were initially picked in crYOLO (Wagner et al., Commun. Biol. 2019) and re-extracted after 2D classification & heterogeneous refinement in cryoSPARC (Punjani et al., Nat. Methods 2017)

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

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

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

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

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ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

The vault associates with membranes in situ.

Geißler K, Kreysing JP, Wang Y, Glushkova D, Obarska-Kosinska A, Hoffmann PC, Böhm S, Schmidt A, Meier-Credo J, Langer JD, Hummer G, Beck M. (2026)