REL
2022-06-23
2022-08-12
2022-08-12
In situ cryo-electron tomography of the C. reinhardtii ciliary transition zone
0000-0003-4247-4303
Ricardo
Diogo
Righetto
Biozentrum, University of Basel
Spitalstrasse 41
Basel
Switzerland
4056
0000-0002-0941-4387
Benjamin
D.
Engel
Biozentrum, University of Basel
Spitalstrasse 41
Basel
Switzerland
4056
van den Hoek H
Klena N
Jordan MA
Alvarez Viar G
Righetto RD
Schaffer M
Erdmann PS
Wan W
Geimer S
Plitzko JM
Baumeister W
Pigino G
Hamel V
Guichard P
Engel BD
302.0
10.6019/EMPIAR-11078
EMDB
molecule
EMD-15262
van den Hoek H
Klena N
Jordan MA
Alvarez Viar G
Righetto RD
Schaffer M
Erdmann PS
Wan W
Geimer S
Plitzko JM
Baumeister W
Pigino G
Hamel V
Guichard P
Engel BD
In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains
Science (New York, N.Y.)
Science
6605
377
543
548
2022
English
10.1126/science.abm6704
35901159
Deconvoluted bin4 tomograms for visualization
/data/bin4_deconvoluted_tomos_forvisualisation
reconstructed volumes
MRC
MRC
20
1
SIGNED 16 BIT INTEGER
928
13.68
928
13.68
Volumes reconstructed in IMOD were deconvoluted using tom_deconv.m:
https://github.com/dtegunov/tom_deconv/blob/master/tom_deconv.m
CTF-corrected bin4 tomograms
/data/bin4_CTFcorrected_tomos_usedinalignments
reconstructed volumes
MRC
MRC
20
1
SIGNED 16 BIT INTEGER
928
13.68
928
13.68
Volumes reconstructed in IMOD at bin4 using phase-flipping for CTF correction.
CTF-corrected bin2 tomograms
/data/bin2_CTFcorrected_tomos_usedinalignments
reconstructed volumes
MRC
MRC
19
1
SIGNED 16 BIT INTEGER
1856
6.84
1856
6.84
Volumes reconstructed in IMOD at bin2 using phase-flipping for CTF correction.
Subtomograms at bin2
/data/subtomograms_bin2
subtomograms
EM
EM
2923
1
32 BIT FLOAT
variable
6.84
variable
6.84
Subtomograms extracted from bin2 tomograms used in alignments and averaging. Each sub-directory contains the particles for a specific structure, namely:
A/ (IFT-A)
B/ (IFT-B)
D/ (IFT-Dynein 1b)
MTD-MIP/
Sleeve/
Stellate/
Y-link/
Aligned tilt series stacks
/data/Tomo1
tilt series
MRC
MRC
20
1
UNSIGNED 16 BIT INTEGER
928
13.68
928
13.68
Drift-corrected, aligned tilt series for each tomogram in a single stack (.ali extension from IMOD)
Unaligned tilt series raw frames
/data/Tomo1/raw_data/raw_frames
micrographs - multiframe
MRC
MRC
20
10
UNSIGNED 16 BIT INTEGER
3838
3.42
3710
3.42
Raw frames from Titan Krios (300 kV, Cs 2.7 mm) equipped with K2 direct electron detector in counting mode and energy filter. The number of frames is variable. In each of the 20 tomogram folders (Tomo1-Tomo20), there is:
Aligned tilt series (.ali file)
raw_data/imod_metadata/ (.defocus, .tlt and .xf metadata files for reconstruction in IMOD)
raw_data/mdocs/ (.mdoc files from SerialEM with data collection information)
raw_data/raw_frames/ (raw frames for individual tilts in MRC format, compressed with bzip2)