EMPIAR-12272 - Rous sarcoma virus frameshifting pseudoknot [multiple data sets in MRC and TIFF formats]

EMPIAR-12272

Rous sarcoma virus frameshifting pseudoknot [multiple data sets in MRC and TIFF formats]

Publication:

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus-programmed ribosomal frameshifting element

Jones CP, Ferré-D'Amaré AR

Proceedings of the National Academy of Sciences of the United States of America 122 (2025)

PMID: 40172966

DOI: 10.1073/pnas.2418418122

Related EMDB entry:

Deposited:

2024-09-05

Released:

2025-06-02

Last modified:

2025-06-02

Imageset size:

4.41 TB

Imageset DOI:

10.6019/EMPIAR-12272

Experimental metadata:

Download xml json

Contains:

picked particles - multiframe - processed
micrographs - multiframe

Image Sets

1. Polished particles used for final reconstruction of Rous sarcoma virus straight dimer

Category:

picked particles - multiframe - processed

Image format:

MRC

No. of images or tilt series:

88523

Image size:

(320, 320)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.83, 0.83)

Details:

Polished particles used for final map reconstruction for Rous sarcoma virus frameshifting pseudoknot straight dimer. These ~85,000 particles were imported into cryoSPARC for homo/NU refinement jobs. This is the RELION job folder.

Files:

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2. Polished particles used for final reconstruction of Rous sarcoma virus bent dimer

Category:

picked particles - multiframe - processed

Image format:

MRC

No. of images or tilt series:

107620

Image size:

(320, 320)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.83, 0.83)

Details:

Polished particles used for final map reconstruction for Rous sarcoma virus frameshifting pseudoknot bent dimer. These ~108,000 particles were imported into cryoSPARC for homo/NU refinement jobs. This is the RELION job folder.

Files:

This entry cannot be downloaded from PDBj.

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We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

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3. Uncurated micrographs for entire dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

10204

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.415, 0.415)

Details:

Uncurated micrographs for the Rous sarcoma virus frameshifting pseudoknot data used to produce particle sets above. Collected at 105,000 magnification, 54.4 e/A2 dose, 50 frames, -0.8-2.0 defocus range on a Titan Krios G1 with Gatan BioQuantum K3 camera and imaging filter (20 eV slit) over 3 days. After motion correction (with 2-fold binning) and CTF estimation in RELION, curation of micrographs produced ~7800 micrographs, from which ~3.4M initial particles were picked with Topaz. Of these, ~400,000 were dimeric particles, which were further classified into "straight" and "bent" particle sets in cryoSPARC. Those were further separated, CTF refined and polished in RELION. These produced the ~88500 straight and ~108000 bent particles also deposited here.

Files:

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