EMPIAR-13662 - The cryo-EM structure of HerA-NurA complex from Thermococcus kodakarensis [multiple data sets in TIFF format]

EMPIAR-13662

The cryo-EM structure of HerA-NurA complex from Thermococcus kodakarensis [multiple data sets in TIFF format]

Publication:

Substrate specificity and action mechanism of the HerA-NurA nuclease from the hyperthermophilic archaeon <i>Thermococcus kodakarensis</i>

Uda K, Yamagami T, Ishino S, Gerle C, Gopalasingam CC, Shigematsu H, Numata T, Ishino Y

mBio 17 (2026)

PMID: 41641993

DOI: 10.1128/mbio.03523-25

Related EMDB entry:

EMD-66465 EMD-66466 EMD-66464 EMD-66462 EMD-66463

Deposited:

2026-03-23

Released:

2026-10-06

Last modified:

2026-10-06

Imageset size:

4.68 TB

Imageset DOI:

10.6019/EMPIAR-13662

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. HN-AMPPNP complex

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4750

Image size:

(4092, 5760)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.794, 0.794)

Details:

- EMD-66462

- Microscope: CRYOARMTM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4 to - 1.6
- Average electron dose per image (e-/A2): 50

- Please use 'CountCDSRef_2021-10-05_19.22.11_194001_3_112-1_0000.mrc' as a gain reference with y-flipping and no rotation.

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2. HN-AMPPNP-dsDNA complex

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5600

Image size:

(4092, 5750)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.752, 0.752)

Details:

- EMD-66463

- Microscope: CRYOARMTM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4 to - 1.6
- Average electron dose per image (e-/A2): 50

- Please use "CountCDSRef_2022-04-26_21.20.01_20220426N11_195-1_0000.mrc" as a gain reference with y-flipping and no rotation.

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. HN-ATPγS-dsDNA complex

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

10350

Image size:

(4092, 5760)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.752, 0.752)

Details:

- EMD-66464 (State 1)
- EMD-66465 (State 2)
- EMD-66466 (State 3)

- Microscope: CRYOARMTM 300
- Detector: Gatan K3 camera
- Acceleration voltage (kV): 300
- Spherical aberration (Cs) : 2.7
- Nominal Defocus (μm): -1.4 to - 1.6
- Average electron dose per image (e-/A2): 50

- Please use "CountCDSRef_2024-02-09_13.36.57_2089_20240206N04_120-1_0000.mrc"

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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A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

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