EMPIAR-11734 - Structure and dynamics of a pentameric KCTD5/Cullin3/GBeta1Gamma2 E3 ubiquitin ligase complex [multiple data sets in MRC and MRCS formats]

EMPIAR-11734

Structure and dynamics of a pentameric KCTD5/Cullin3/GBeta1Gamma2 E3 ubiquitin ligase complex [multiple data sets in MRC and MRCS formats]

Publication:

Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex.

Nguyen DM, Rath DH, Devost D, Pétrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hébert TE, Privé GG

Proceedings of the National Academy of Sciences of the United States of America 121 (2024)

PMID: 38625940

DOI: 10.1073/pnas.2315018121

Related EMDB entry:

EMD-42011 EMD-41998 EMD-42000 EMD-42001 EMD-41997 EMD-41995 EMD-41999 EMD-42003 EMD-42010 EMD-41996 EMD-42004 EMD-42008 EMD-41994 EMD-42007 EMD-42006 EMD-42002 EMD-42005 EMD-42009

Deposited:

2023-09-20

Released:

2023-10-31

Last modified:

2023-10-31

Imageset size:

5.40 TB

Imageset DOI:

10.6019/EMPIAR-11734

Experimental metadata:

Download xml json

Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

MRC movies (FoilHole_*_Data_*_Fractions.mrc in KriosData) in this entry were compressed by bzip2 (pbzip2)
by EMPIAR Japan to save space and bandwidth.

Some programs (e.g. RELION >= 4.0.1 and CryoSPARC) can process compressed movies without explicit
decompression. For other programs, movies have to be decompressed beforehand. In this case,
you might want to convert decompressed MRC movies into TIFF to save your local storage.

Original size:   8,523,199,560 kilobytes
Compressed size: 5,165,107,866 kilobytes

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - processed

Image Sets

1. K5C3Gbg1 Krios Data Grid 1 multiframe micrographs

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

432

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.03, 1.03)

Details:

Collected on Falcon 4i. Calibrated pixel size is 1.03 which differs from the header information. Folder also contains link information linking the file names to the downstream processed frames.

Files:

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. K5C3Gbg1 Krios Data Grid 2 multiframe micrographs

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

4199

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.03, 1.03)

Details:

Collected on Falcon 4i. Calibrated pixel size is 1.03 which differs from the header information.

Files:

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. K5C3Gbg Krios Data Grid 2 TILT multiframe micrographs. Collected with 40 degree tilt.

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

4039

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.03, 1.03)

Details:

Collected on Falcon 4i. Calibrated pixel size is 1.03 which differs from the header information. Collected with 40 degree tilt.

Files:

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. MotionCorrected Data for normal(Grid1+Grid2) K5C3Gbg

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

4367

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.03, 1.03)

Details:

Patch_aligned_doseweighted

Files:

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. MotionCorrected Data for K5C3Gbg Grid2 TILT

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

4039

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.03, 1.03)

Details:

Patch_aligned_doseweighted of the Tilted Data set

Files:

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. K5C3Gbg Particles

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

6918

Image size:

(324, 324)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.03, 1.03)

Details:

Particles picked from Patch aligned doseweighted motion corrected images. Particles are from both the standard and tilted images.

Files:

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

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

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

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)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (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)

See all citations

Protein Data Bank Japan News

[2024-11-13]

236 new PDB entries have been released on 2024-11-13.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024