EMPIAR-11844 - Cryo-EM of Tetrahymena ribozyme [multiple data sets in TIFF and MRC formats]

EMPIAR-11844

Cryo-EM of Tetrahymena ribozyme [multiple data sets in TIFF and MRC formats]

Publication:

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

Kretsch RC, Li S, Pintilie G, Palo MZ, Case DA, Das R, Zhang K, Chiu W

bioRxiv (2025)

DOI: 10.1101/2025.01.23.634578

Related EMDB entry:

EMD-42499 EMD-42498

Deposited:

2023-11-28

Released:

2025-02-04

Last modified:

2025-02-04

Imageset size:

3.65 TB

Imageset DOI:

10.6019/EMPIAR-11844

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs of tetrahymena ribozyme.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

18366

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.82, 0.82)

Details:

These micrographs were collected with a Titan Krios G3i, 300kV and a K3 detector. Over the collection, the sample was exposed evenly to 57.25 electrons per angstrom squared with a total exposure time of 2.5 seconds. Desired defocuses ranged from -0.5 to -2 nm. The exposures are not gain corrected, the gain reference can be found at data/ThR/exposures/K3-18210041 Gain Ref. x1.m1.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. Extracted particles and orientations for final reconstruction of tetrahymena ribozyme.

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

1181000

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.82, 0.82)

Details:

Particles extracted from motion-corrected micrographs. The orientations for the final reconstruction can be found in data/ThR/particles/2.2A_cryosparc_P5_J1222_004_particles.cs and data/ThR/particles/2.3A_cryosparc_P5_J1224_004_particles.cs

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

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

[2025-02-19]

209 new PDB entries have been released on 2025-02-19.

[2025-01-30]

[wwPDB] Take the PDBx/mmCIF User Guide Survey and Win!

[2025-01-17]

[wwPDB] PDB-Dev now PDB-IHM

[2025-01-09]

[wwPDB] Time-stamped Copies of PDB and EMDB Archives

[2024-11-28]

[wwPDB] Access SDF/MOL formatted CCD files from the PDB archive