EMPIAR-13345
Single-particle cryo-EM structures of E. coli 70S ribosomes, WT and mutants with trapped RNA conformational ground and excited states [multiple data sets in TIFF and MRC formats]
Publication:

Universal 3D Motif dynamics in RNA: The A-minor Switch

Steinmetzger C, Karlsson H, Fontana C, Galindo Riera N, Riad M, Kosek D, Schlagnitweit J, Steiner E, Sandoz SF, Andersson ER, Petzold K

bioRxiv (2026)

Deposited:
2025-12-09
Released:
2026-05-31
Last modified:
2026-05-31
Imageset size:
16.57 TB
Imageset DOI:
Experimental metadata:
Download xml json
Contains:
  • micrographs - multiframe
  • picked particles - single frame - processed
1. Unaligned multi-frame micrographs of E. coli 70S ribosome
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
15518
Image size:
(5760, 4092)
Pixel type:
UNSIGNED BYTE
Pixel spacing:
(0.505, 0.505)
Details:
Movies were collected using a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV equipped with a K3 BioQuantum detector (Gatan) at the Karolinska Institutet 3D-EM facility in Solna, Sweden. The data was acquired using EPU software (Thermo Fisher Scientific) with a pixel size of 0.505 Å/px (nominal magnification 165000x), electron dose of ~50 e−/Å2, 50 frames per movie, and a defocus range of −0.3 to −2.0 µm.

The movies are gain-corrected.
Files:
Loading...
2. PDB 9TMI / EMD-56070: E. coli 70S ribosome with A- and P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
73907
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
3. EMD-56834: E. coli 70S ribosome with P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
97445
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
4. EMD-56835: E. coli 70S ribosome without tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
166130
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
5. PDB 9TNL / EMD-56091: E. coli 70S ribosome with A/P- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
69415
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
6. EMD-56836: E. coli 70S ribosome with A- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
49259
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
7. EMD-56837: E. coli 70S ribosome with P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
34872
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
8. Unaligned multi-frame micrographs of E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
18448
Image size:
(5760, 4092)
Pixel type:
UNSIGNED BYTE
Pixel spacing:
(0.505, 0.505)
Details:
Movies were collected using a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV equipped with a K3 BioQuantum detector (Gatan) at the Karolinska Institutet 3D-EM facility in Solna, Sweden. The data was acquired using EPU software (Thermo Fisher Scientific) with a pixel size of 0.505 Å/px (nominal magnification 165000x), electron dose of ~50 e−/Å2, 50 frames per movie, and a defocus range of −0.3 to −2.0 µm.

The movies are gain-corrected.
Files:
Loading...
9. PDB 9TQA / EMD-56128: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
81491
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
10. EMD-56839: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
86813
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
11. EMD-56840: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, without tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
72339
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
12. PDB 28UH / EMD-56827: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
75660
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
13. EMD-56841: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
53199
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
14. EMD-56842: E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
38095
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
15. Unaligned multi-frame micrographs of E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
19249
Image size:
(5760, 4092)
Pixel type:
UNSIGNED BYTE
Pixel spacing:
(0.505, 0.505)
Details:
Movies were collected using a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV equipped with a K3 BioQuantum detector (Gatan) at the Karolinska Institutet 3D-EM facility in Solna, Sweden. The data was acquired using EPU software (Thermo Fisher Scientific) with a pixel size of 0.505 Å/px (nominal magnification 165000x), electron dose of ~50 e−/Å2, 50 frames per movie, and a defocus range of −0.3 to −2.0 µm.

The movies are gain-corrected.
Files:
Loading...
16. PDB 28UI / EMD-56828: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
80169
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
17. EMD-56843: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
85044
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
18. EMD-56844: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, without tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
84558
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
19. PDB 28UJ / EMD-56829: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
62030
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
20. EMD-56845: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
39381
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
21. EMD-56846: E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
36302
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7585
Files:
Loading...
22. Unaligned multi-frame micrographs of E. coli 70S ribosome, conformational ground state mutation in SSU-h41
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
5412
Image size:
(5760, 4092)
Pixel type:
UNSIGNED BYTE
Pixel spacing:
(0.505, 0.505)
Details:
Movies were collected using a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV equipped with a K3 BioQuantum detector (Gatan) at the Karolinska Institutet 3D-EM facility in Solna, Sweden. The data was acquired using EPU software (Thermo Fisher Scientific) with a pixel size of 0.505 Å/px (nominal magnification 165000x), electron dose of ~50 e−/Å2, 50 frames per movie, and a defocus range of −0.3 to −2.0 µm.

The movies are gain-corrected.
Files:
Loading...
23. PDB 28UK / EMD-56830: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
23232
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
24. EMD-56847: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
36584
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
25. EMD-56848: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, without tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
31773
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
26. PDB 28UL / EMD-56831: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A/P- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
13469
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
27. EMD-56849: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
3152
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
28. EMD-56850: E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
10172
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
29. Unaligned multi-frame micrographs of E. coli 70S ribosome, conformational excited state mutation in SSU-h41
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
6193
Image size:
(5760, 4092)
Pixel type:
UNSIGNED BYTE
Pixel spacing:
(0.505, 0.505)
Details:
Movies were collected using a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV equipped with a K3 BioQuantum detector (Gatan) at the Karolinska Institutet 3D-EM facility in Solna, Sweden. The data was acquired using EPU software (Thermo Fisher Scientific) with a pixel size of 0.505 Å/px (nominal magnification 165000x), electron dose of ~50 e−/Å2, 50 frames per movie, and a defocus range of −0.3 to −2.0 µm.

The movies are gain-corrected.
Files:
Loading...
30. PDB 28UM / EMD-56832: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
34748
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
31. EMD-56851: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
34669
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
32. EMD-56852: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, without tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
58515
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
33. PDB 28UN / EMD-56833: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A/P- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
14786
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
34. EMD-56853: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
4860
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...
35. EMD-56854: E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P/E-site tRNA
Category:
picked particles - single frame - processed
Image format:
MRC
No. of images or tilt series:
9271
Image size:
(576, 576)
Pixel type:
16 BIT FLOAT
Pixel spacing:
(0.7575, 0.7575)
Details:
Particle stack after 3D classification, reference-based motion correction, 3D variability analysis. With local + global CTF refinement and negative EWS correction.

Pixel size after calibration against PDB 4YBB is 0.7575
Files:
Loading...