EMPIAR-12960 - Cryo-EM micrographs of R2Tg retrotransposon initiating target-primed reverse transcription [10628 multi-frame micrographs composed of 40 frames each in TIFF format]

EMPIAR-12960

Cryo-EM micrographs of R2Tg retrotransposon initiating target-primed reverse transcription [10628 multi-frame micrographs composed of 40 frames each in TIFF format]

Publication:

Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons

Edmonds KK, Wilkinson ME, Strebinger D, Chen H, Lash B, Schaefer CC, Zhu S, Liu D, Zilberzwige-Tal S, Ladha A, Walsh ML, Frangieh CJ, Vaz Reay NA, Macrae RK, Wang X, Zhang F

Nature communications 16 (2025)

PMID: 40603868

DOI: 10.1038/s41467-025-61321-z

Related EMDB entry:

EMD-47091

Deposited:

2025-09-08

Released:

2025-11-30

Last modified:

2025-11-30

Imageset size:

1.68 TB

Imageset DOI:

10.6019/EMPIAR-12960

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned multi-frame movies of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

10628

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.663, 0.663)

Details:

RAW MICROGRAPHS AND REFINEMENT STAR FILE FOR R2Tg TPRT COMPLEX (EMD-47091; PDB 9DOU)
Data collected at MIT.nano on Thermo Scientific Titan Krios G3i cryo-TEM

Voltage 300 keV
Camera Gatan K3, super-resolution mode with 2-fold binning by EPU
Energy filter GIF, 20eV slit width
Magnification 130000
Pixel size 0.663 A/pix
Dose 59.6 e/A2
Exposure rate 25.7 e/pix/s
Exposure time 1.02 s
Fractions 40

Total mics 10628

GainReference.mrc was binned using 'rebin by two' in Digital Micrograph. It needs to be flipped for use in RELION motion correction (Gain flip: Flip upside down (1) ). It can probably be used as is for cryoSPARC.

particles.star contains metadata for the particle selected for the final reconstruction.

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

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)

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)

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (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)

Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

Localization of macromolecules in crowded cellular cryo-electron tomograms from extremely sparse labels.

Uddin MR, Ahmed AY, Tabib HMS, Tahmid MT, Alam MZU, Freyberg Z, Xu M. (2025)

Structural insight into bicarbonate-mediated carboxylation by human vitamin K-dependent carboxylase.

Wu K, Wang Z, Yao D, Li S, Wang X, Zhang Y, Cao M, Shen Y, Xing S, Wu J, Lei M, Lan P. (2025)

Conserved hydrophilic checkpoints tune FocA-mediated formate:H<sup>+</sup> symport.

Tüting C, Janson K, Kammel M, Ihling C, Lorenz J, Kyrilis FL, Hamdi F, Erdmann C, Sinz A, Sawers RG, Kastritis PL. (2025)

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2025)

See all citations

Protein Data Bank Japan News

[2025-12-10]

370 new PDB entries have been released on 2025-12-10.

[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

[2025-09-26]

[wwPDB] Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report

[2025-07-17]

[wwPDB] Transitioning to PDBx/mmCIF and Extended PDB IDs

[2025-06-25]

[wwPDB] Extension to EMDB Accession Codes

[2025-04-18]

[wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

[2025-03-25]

Announcement of the PDBj Newsletter Vol.25 release

[2025-03-11]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

See all news