EMPIAR-12928 - Cas1-2/3 integration complex, 34 bp foreign DNA with PAM, CRISPR leader-repeat-spacer DNA fragment [multiple data sets in TIFF format]

EMPIAR-12928

Cas1-2/3 integration complex, 34 bp foreign DNA with PAM, CRISPR leader-repeat-spacer DNA fragment [multiple data sets in TIFF format]

Publication:

Structures reveal how the Cas1-2/3 integrase captures, delivers, and integrates foreign DNA into CRISPR loci

Henriques WS, Bowman J, Hall LN, Gauvin CC, Wei H, Kuang H, Zimanyi CM, Eng ET, Santiago-Frangos A, Wiedenheft B

bioRxiv (2025)

PMID: 40661357

DOI: 10.1101/2025.06.10.658980

Related EMDB entry:

EMD-71101 EMD-71112

Deposited:

2025-08-11

Released:

2025-11-04

Last modified:

2025-11-04

Imageset size:

9.13 TB

Imageset DOI:

10.6019/EMPIAR-12928

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. 1/5 Unaligned multi-frame micrographs of the Cas1-2/3 heterohexameric complex bound to a 34 bp fragment of dsDNA with a PAM and to a dsDNA fragment containing the CRISPR leader, repeat, and spacer

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1756

Image size:

(5760, 4092)

Pixel type:

SIGNED BYTE

Pixel spacing:

(1.152, 1.152)

Details:

Movies were acquired using a Gatan K3 direct electron detector, operated in electron counting mode targeting a total electron exposure of 65.67 e-/Å2 over 50 frames (5.992 second exposure, 0.12 second frame time). The SerialEM data collection software was used to collect micrographs at 36,000x nominal magnification (1.152 Å/pixel at the specimen level) over a defocus range of -0.5 µm to -2.0 µm. Movies were gain-corrected on the microscope server so no gain reference is provided.

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)

2. 2/5 Unaligned multi-frame micrographs of the Cas1-2/3 heterohexameric complex bound to a 34 bp fragment of dsDNA with a PAM and to a dsDNA fragment containing the CRISPR leader, repeat, and spacer

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1841

Image size:

(5760, 4092)

Pixel type:

SIGNED BYTE

Pixel spacing:

(1.152, 1.152)

Details:

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)

3. 3/5 Unaligned multi-frame micrographs of the Cas1-2/3 heterohexameric complex bound to a 34 bp fragment of dsDNA with a PAM and to a dsDNA fragment containing the CRISPR leader, repeat, and spacer

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3759

Image size:

(5760, 4092)

Pixel type:

SIGNED BYTE

Pixel spacing:

(1.152, 1.152)

Details:

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)

4. 4/5 Unaligned multi-frame micrographs of the Cas1-2/3 heterohexameric complex bound to a 34 bp fragment of dsDNA with a PAM and to a dsDNA fragment containing the CRISPR leader, repeat, and spacer

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2055

Image size:

(5760, 4092)

Pixel type:

SIGNED BYTE

Pixel spacing:

(1.152, 1.152)

Details:

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)

5. 5/5 Unaligned multi-frame micrographs of the Cas1-2/3 heterohexameric complex bound to a 34 bp fragment of dsDNA with a PAM and to a dsDNA fragment containing the CRISPR leader, repeat, and spacer

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

995

Image size:

(11520, 8184)

Pixel type:

SIGNED BYTE

Pixel spacing:

(0.576, 0.576)

Details:

Movies were acquired using a Gatan K3 direct electron detector, operated in electron counting mode targeting a total electron exposure of 65.67 e-/Å2 over 50 frames (5.992 second exposure, 0.12 second frame time). The SerialEM data collection software was used to collect micrographs at 36,000x nominal magnification (1.152 Å/pixel at the specimen level, collected in super-resolution mode with a physical pixel size of 0.576 A/pixel.) over a defocus range of -0.5 µm to -2.0 µm. Movies were gain-corrected on the microscope server so no gain reference is provided.

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)

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

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)

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)

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)

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

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

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