EMPIAR-11823 - Cryo-EM of the human CAK: Data for 1.73 Å-resolution reconstruction [multiple data sets in EER format]

EMPIAR-11823

Cryo-EM of the human CAK: Data for 1.73 Å-resolution reconstruction [multiple data sets in EER format]

Publication:

High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design

Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJ

Nature communications 15 (2024)

PMID: 38480681

DOI: 10.1038/s41467-024-46375-9

Related EMDB entry:

EMD-17522

Deposited:

2023-12-05

Released:

2024-05-20

Last modified:

2024-05-20

Imageset size:

12.13 TB

Imageset DOI:

10.6019/EMPIAR-11823

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. EER movies, CAK-ICEC0943, grid VC1-1

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5729

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220312_VC1-1/).

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. EER movies, CAK-ICEC0768, grid VC2-4

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5583

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220312_VC2-4/).

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. EER movies, CAK-dinaciclib, grid VC4-3

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5210

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220128_ICR_VC4-3/).

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. EER movies, CAK-BS181, grid VC8-1

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5203

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220311_VC8-1/).

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. EER movies, CAK-ICEC0942, grid VC13-1

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5231

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220129_VC13-3/). This dataset was only used for the high-resolution (1.73 Å) reconstruction, not for interpretation of inhibitor interactions described in the manuscript.

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)

6. EER movies, CAK-ICEC0942, grid VC14-1

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5367

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.57, 0.57)

Details:

EER movies. The gain reference can be found in the top directory (data/Krios3_220409_ICR_VC14-1/). This dataset was used both for the high-resolution (1.73 Å) reconstruction and for interpretation of inhibitor interactions described in the manuscript.

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

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)

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM.

Fan X, Zhang Q, Zhang H, Zhu J, Ju L, Shi Z, Hu M, Bao C. (2024)

Self-assembled superstructure alleviates air-water interface effect in cryo-EM.

Zheng L, Xu J, Wang W, Gao X, Zhao C, Guo W, Sun L, Cheng H, Meng F, Chen B, Sun W, Jia X, Zhou X, Wu K, Liu Z, Ding F, Liu N, Wang HW, Peng H. (2024)

See all citations

Protein Data Bank Japan News

[2024-09-04]

375 new PDB entries have been released on 2024-09-04.

[2024-08-28]

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

[2024-08-15]

[wwPDB] PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

[2024-06-19]

[wwPDB] Announcing the New PDBx/mmCIF User Guide

[2024-06-11]

[wwPDB] Paper Published on NextGen Archive