EMPIAR-10697 - Cryo-EM structures of human RNA Polymerase III [multiple data sets in TIFF and MRCS formats]

EMPIAR-10697

Cryo-EM structures of human RNA Polymerase III [multiple data sets in TIFF and MRCS formats]

Publication:

Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states

Girbig M, Misiaszek AD, Vorländer MK, Lafita A, Grötsch H, Baudin F, Bateman A, Müller CW

Nature structural & molecular biology 28 (2021) 210-219

PMID: 33558764

DOI: 10.1038/s41594-020-00555-5

Related EMDB entry:

EMD-11742 EMD-11736 EMD-11738 EMD-11673 EMD-11740 EMD-11737 EMD-11739 EMD-11741

Deposited:

2020-10-21

Released:

2021-05-07

Last modified:

2021-05-07

Imageset size:

3.27 TB

Imageset DOI:

10.6019/EMPIAR-10697

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. LZW-TIFF compressed multiframe micrographs of human RNA Pol III EC

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9488

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.05, 1.05)

Details:

Micrographs were recorded in counting mode, dose = 1.01 e/A^2/frame
Defocus range = 0.75 - 2.00
CountRef_41-1_00001.mrc to be found in "data/EMPIAR/Human_Pol_III_EC/01_raw_tiffs/"

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. Initially picked particles of human RNA Pol III EC

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

367717

Image size:

(250, 250)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.05, 1.05)

Details:

Directory "data/EMPIAR/Human_Pol_III_EC/02__initially_picked_particles" also contains the "run_data.star" file, which contains the coordinates of the particles that went into the final 3D reconstruction of human Pol III EC (unpolished)

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. Polished particles of human RNA Pol III EC (final reconstruction)

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

166071

Image size:

(440, 440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.05, 1.05)

Details:

Directory "data/EMPIAR/Human_Pol_III_EC/03_polished_particles_map_B" contains the "run_data.star" file of the final 3D reconstruction derived from Relion 3D Refinement after particle polishing and CTF refinement

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. LZW-TIFF compressed multiframe micrographs of human RNA Pol III apo

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9544

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.822, 0.822)

Details:

Micrographs were recorded in counting mode, dose = 0.95 e/A^2/frame
Defocus range = 0.75 - 2.25
CountRef_51-1_00001.mrc to be found in "data/EMPIAR/Human_Pol_III_apo/01_raw_tiffs/"

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. Initially picked particles of human RNA Pol III apo

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

304683

Image size:

(328, 328)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.822, 0.822)

Details:

Directory "data/EMPIAR/Human_Pol_III_apo/02_initially_picked_particles" also contains the "run_data.star" file, which contains the coordinates of the particles that went into the final 3D reconstruction of human Pol III apo (unpolished)

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. Polished particles of human RNA Pol III apo (final reconstruction)

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

111289

Image size:

(440, 440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.822, 0.822)

Details:

Directory "data/EMPIAR/Human_Pol_III_apo/03_polished_particles_map_A" contains the "run_data.star" file of the final 3D reconstruction derived from Relion 3D Refinement after particle polishing and CTF refinement

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