EMPIAR-13661 - Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus [multiple data sets in TIFF format]

EMPIAR-13661

Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus [multiple data sets in TIFF format]

Publication:

Sequential structural rearrangements at the PAM-distal site of a type I-F3 CRISPR-Cas effector enabling RNA-guided DNA transposition

Ishihara K, Matsumoto S, Gerle C, Gopalasingam CC, Shigematsu H, Shirai T, Numata T

Nucleic acids research 54 (2026)

PMID: 41495894

DOI: 10.1093/nar/gkaf1415

Related EMDB entry:

EMD-65340 EMD-65339 EMD-65338

Deposited:

2026-03-23

Released:

2026-10-06

Last modified:

2026-10-06

Imageset size:

4.33 TB

Imageset DOI:

10.6019/EMPIAR-13661

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. TniQ-Cascade-dsDNA PR state

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5150

Image size:

(4092, 5760)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.752, 0.752)

Details:

- Microscope: CRYOARM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4, -1.6
- Average electron dose per image (e-/A2): 50
- Please use "CountCDSRef_2023-12-15_20.54.07_231215IK03_127-13_0000.mrc" as a gain reference

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2. TniQ-Cascade-dsDNA FR1 state

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

8800

Image size:

(4092, 5750)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.752, 0.752)

Details:

- Microscope: CRYOARM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4, -1.6
- Average electron dose per image (e-/A2): 50
- Please use "CountCDSRef_2024-12-04_16.53.50_2812_129-1_0000.mrc" as a gain reference

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. TniQ-Cascade-dsDNA FR2 state

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7926

Image size:

(4092, 5760)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.752, 0.752)

Details:

- Microscope: CRYOARM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4, -1.6
- Average electron dose per image (e-/A2): 50
- Please use "CountCDSRef_2024-12-04_16.53.50_2812_129-1_0000.mrc" as a gain reference

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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Burton Smith RN, Murata K. (2026)

Structural heterogeneity of CTE Type I tau filaments with an interface-shifted polymorph

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Ligand-induced activation of RyR1 in native membranes.

Mikirtumov V, Golusik S, Huo R, Sprink T, Balyschew N, Yang W, Diebolder C, Yuan S, Kotecha A, Kudryashev M. (2026)

QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning.

Sun Y, Zhao J, Xu N, Wang L, Ding W, Li M. (2026)

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Li F, Dong H, Tang S, Wang X, Zhang C, Ji C, Han R, Zhang F, Wan X. (2026)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (2026)

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Ramírez-Aportela E, Zarrabeitia OL, Fonseca YC, Ceska T, Subramaniam S, Carazo JM, Sorzano COS. (2026)

Helical reconstruction of amyloids in cryoSPARC.

Schaefer JH, O'Neill RT, Donnelly JP, Powers ET, Kelly JW, Lander GC. (2026)

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)

See all citations

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