EMPIAR-11481 - Movies of GroEL-ES-nucleotide complex plunged 13, 50, 200 ms and 20 s after mixing with ATP [multiple data sets in TIFF format]

EMPIAR-11481

Movies of GroEL-ES-nucleotide complex plunged 13, 50, 200 ms and 20 s after mixing with ATP [multiple data sets in TIFF format]

Publication:

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting

Torino S, Dhurandhar M, Stroobants A, Claessens R, Efremov RG

Nature Methods (---)

DOI: 10.1038/s41592-023-01967-z

Related EMDB entry:

EMD-16117 EMD-16106 EMD-16119 EMD-16115 EMD-16108 EMD-16154 EMD-16116 EMD-16118 EMD-16100 EMD-16099 EMD-16107 EMD-16125 EMD-16102 EMD-16109

Deposited:

2023-02-08

Released:

2023-08-18

Last modified:

2023-08-18

Imageset size:

2.94 TB

Imageset DOI:

10.6019/EMPIAR-11481

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. GroELES with 20s of mixing time

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4194

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

STAR files associated with the reconstructed maps from this dataset are uploaded in the directory 'associated_star_files' with names 20sGroEL-ATP.star, 20sGroEL-ATP-GroES.star, 20sGroEL-ATP-ADP-GroES.star and 20s_GroEL-ATP-2GroES.star

gain files are included in the Gain file directory under particular time point. Please use the corresponding gain file by matching the gain file date and micrograph date.
The dates are in format YYYYMMDD
The date is indicated at the start of micrograph name e.g 20220628_trGroEL...tif
The date is the second part of gain refence file name e.g CountRef_20220628_trGroEL...mrc

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. GroELES at 50ms timepoint

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1416

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

STAR files associated with the reconstructed maps from this dataset are uploaded in the directory 'associated_star_files' with names 50ms_GroEL-ADP.star, 50ms_GroEL-ATP-ADP.star, 50ms_GroEL-ATP.star

gain files are included in the Gain file directory under particular time point. Please use the corresponding gain file by matching the gain file date and micrograph date.
The dates are in format YYYYMMDD
The date is indicated at the start of micrograph name e.g 20220628_trGroEL...tif
The date is the second part of gain refence file name e.g CountRef_20220628_trGroEL...mrcGroEL was mixed with GroES and ATP and plunged within 50ms

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. GroEL 13ms timepoint

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2609

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

STAR files associated with the reconstructed maps from this dataset are uploaded in the directory 'associated_star_files' with names 13ms_GroEL-ADP.star, 13ms-GroEL-ATP-ADP.star, 13ms_GroEL-ATP.star

gain files are included in the Gain file directory under particular time point. Please use the corresponding gain file by matching the gain file date and micrograph date.
The dates are in format YYYYMMDD
The date is indicated at the start of micrograph name e.g 20220628_trGroEL...tif
The date is the second part of gain refence file name e.g CountRef_20220628_trGroEL...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)

4. GroELES 200ms timepoint

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5445

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

STAR files associated with the reconstructed maps from this dataset are uploaded in the directory 'associated_star_files' with names 200msGroEL-ATP.star, 200msGroEL-ATP-GroES.star, 200msGroEL-ATP-ADP-GroES.star and 200ms_GroEL-ATP-2GroES.star

gain files are included in the Gain file directory under particular time point. Please use the corresponding gain file by matching the gain file date and micrograph date.
The dates are in format YYYYMMDD
The date is indicated at the start of micrograph name e.g 20220628_trGroEL...tif
The date is the second part of gain refence file name e.g CountRef_20220628_trGroEL...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)

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

Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase.

Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS. (2023)

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.

Rigden DJ, Fernández XM. (2023)

EMPIAR: the Electron Microscopy Public Image Archive.

Iudin A, Korir PK, Somasundharam S, Weyand S, Cattavitello C, Fonseca N, Salih O, Kleywegt GJ, Patwardhan A. (2023)

CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM.

Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y. (2023)

Structure of a RecT/Redβ family recombinase in complex with a duplex intermediate of DNA annealing.

Caldwell BJ, Norris AS, Karbowski CF, Wiegand AM, Wysocki VH, Bell CE. (2022)

See all citations

Protein Data Bank Japan News

[2024-05-01]

288 new PDB entries have been released on 2024-05-01.

[2024-04-09]

[wwPDB] CASP16 Call for Targets

[2024-04-02]

Announcement of the PDBj Newsletter Vol.24 release

[2024-03-21]

[wwPDB] Paper Published on NMR Restraint Validation

[2024-03-13]

[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations

[2024-03-06]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2024-02-15]

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

[2024-02-13]

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

[2024-02-06]

[wwPDB] Preprint Published on NMR Restraint Validation

[2024-02-05]

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

See all news