EMPIAR-12094 - Structural basis for translational control by the human 48S initiation complex [multiple data sets in MRC and MRCS formats]

EMPIAR-12094

Structural basis for translational control by the human 48S initiation complex [multiple data sets in MRC and MRCS formats]

Publication:

Structural basis for translational control by the human 48S initiation complex

Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N

Nature structural & molecular biology 32 (2024) 62-72

PMID: 39289545

DOI: 10.1038/s41594-024-01378-4

Related EMDB entry:

EMD-17696 EMD-17698 EMD-17699 EMD-17697 EMD-17700 EMD-17701 EMD-19128

Deposited:

2024-02-16

Released:

2025-05-04

Last modified:

2025-05-04

Imageset size:

6.86 TB

Imageset DOI:

10.6019/EMPIAR-12094

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
picked particles - single frame - processed

Image Sets

1. Motion-corrected, dose-weighted micrographs

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

93510

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.16, 1.16)

Details:

Micrographs were obtained from movie-stacks of 20 frames à 2-2.5 e/A^2 by global motion-correction and dose-weighting using Relion 4.0, CTF parameters were estimated with GCTF 1.06 and particles were selected by GAUTOMATCH 0.56.
- Micrographs star-file (Micrographs with FinalResolution better 4.5A): data/corrected_micrographs.star
- Particle coordinates: data/corrected_micrographs/*_automatch.star

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. Shiny particles, obtained by Bayesian polishing in Relion 4.0

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

1308019

Image size:

(360, 360)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.16, 1.16)

Details:

Star-files for individual particle populations are located in data/particles (see below), masks used for sorting and final refinements in data/particles/masks360.
Star-file for all shiny particles:
- data/shiny_particles360_all.star
Star-files for shiny particles of major states
- data/particles/shiny_particles360_48S-1.star
- data/particles/shiny_particles360_48S-2.star
- data/particles/shiny_particles360_48S-3.star
- data/particles/shiny_particles360_48S-4.star
- data/particles/shiny_particles360_48S-5.star
Star-files for shiny particles of eIF2, tRNA and eIFB5 substates:
- data/particles/shiny_particles360_48S-2-1.star
- data/particles/shiny_particles360_48S-2-2.star
- data/particles/shiny_particles360_48S-2-3.star
- data/particles/shiny_particles360_48S-3-1.star
- data/particles/shiny_particles360_48S-3-2.star
- data/particles/shiny_particles360_48S-3-3.star
- data/particles/shiny_particles360_48S-4-1.star
- data/particles/shiny_particles360_48S-4-2.star
- data/particles/shiny_particles360_48S-5-1.star
- data/particles/shiny_particles360_48S-5-2.star
- data/particles/shiny_particles360_48S-5-3.star
Star-files for shiny particles of eIF3bi substates:
- data/particles/shiny_particles360_48S-1_eIF3bi_majorstate.star
- data/particles/shiny_particles360_closed48S_eIF3bi_majorstate.star
- data/particles/shiny_particles360_closed48S_eIF3bi_minorstate1.star
- data/particles/shiny_particles360_closed48S_eIF3bi_minorstate2.star

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. Signal-subtracted particles - eIF3core in open 48S

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

92749

Image size:

(240, 240)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.16, 1.16)

Details:

Star-files with subtracted particles used for local refinement of eIF3core in open 48S (48S-1):
- data/subtracted_particles/subtracted_particles240_eIF3core_open48S.star
Masks used for refinements are located in data/subtracted_particles/masks240.

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. Signal-subtracted particles - eIF3core in closed 48S

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

356632

Image size:

(240, 240)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.16, 1.16)

Details:

Star-files with subtracted particles used for local refinement of eIF3core in closed 48S (48S-2 to 5):
- data/subtracted_particles/subtracted_particles240_eIF3core_closed48S.star
Masks used for refinements are located in data/subtracted_particles/masks240.

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

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

'authorString'

See all citations

Protein Data Bank Japan News

[2025-11-19]

[wwPDB] Coming soon: wwPDB Data Processing Distribution Changes

[2025-11-19]

318 new PDB entries have been released on 2025-11-19.

[2025-10-30]

[wwPDB] Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

[2025-09-26]

[wwPDB] Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report

[2025-07-17]

[wwPDB] Transitioning to PDBx/mmCIF and Extended PDB IDs

[2025-06-25]

[wwPDB] Extension to EMDB Accession Codes

[2025-04-18]

[wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

[2025-03-25]

Announcement of the PDBj Newsletter Vol.25 release

[2025-03-11]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2025-03-10]

[wwPDB] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models

See all news