2018-08-22 REL PDBe PDBe PDBe 2016-12-24 2017-01-25 2018-08-22 2018-08-22 Busselez J Chichon FJ Melero R Carrascosa JL Carazo JM Busselez J Chichon FJ Rodriguez MJ Alpizar A Gharbi SI Franch M Melero R Paradela A Carrascosa JL Carazo JM To Be Published 0353 EMD-3557 other EM volume

Centriolar distal MT doublet from a mammal centrosome. Centrosomes were extracted from o.aries thymocytes.

EMD-3558 associated EM volume Centrosome enriched from young lamb thymocytes Centrosome enriched from young lamb thymocytes 0

The centrosome were extracted accordingly to Komesli et al. 1989

Ovis aries Thymus Thymus Lobules Centrosome cytoplasm near the nucleus 230000 subtomogramAveraging particle 0.076 7.2 10.0 C8H18N2O6S2 Pipes

pH rectification with KOH

quantifoil 3.5/1 COPPER/RHODIUM 300 FORMVAR HOLEY GLOW DISCHARGE ETHANE LEICA EM CPC

The sample was enriched by two step of sedimentation in sucrose gradient. The sucrose was washed out in several drops of buffer, the last of which included fiducial markers (10 nm bovine serum albumin (BSA)-coated gold beads) for tilt series alignment

FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 2.0 5.0 5.54 5.0 5.906 42000. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Gatan 968 Quantum -10 10 GATAN K2 QUANTUM (4k x 4k) 3838 3710 1.0 1.4 1

Tilt series were aligned based on fiducials with IMOD and mass normalized using PRIISM. The ctf correction was processed on tilt series using TomoCTF. Tomogram were reconstructed using SIRT algorithm with TOMO3D. The number of frames per image were variable, with 8 frames at full tilt, through to 4 frames at zero tilt.

2 FOURIER SPACE 47.0 FSC 0.5 CUT-OFF Dynamo 1.1.22 282 4 800 volume picked interactively Dynamo 1.1.22

Coarse models of the centriole microtubules were obtained using Fiber Tracing in Amira and converted for import in dynamo. From those coarse models, "filament with torsion" models were traced in dynamo. The triplets were segregated from the doublets and triplets volume particle were windowed with overlap every 8.3nm along the "filament with torsion" models

TOMOCTF

wiener filtering, made on tilt series

4 Dynamo 1.1.22

classification by PCA + k-means

OTHER Dynamo 1.1.22

The particular geometry of the centriole with its repeat every 8.3nm along the proximal-distal axis and its coarse 9 fold symmetry was used to construct from each tomogram a model lowly affected by missing wedge. Those coarse models were volume aligned and an initial reference were averaged from all the subtomogram particle using the coarse orientation of the particles determined that way. This model was iteratively refined. The reference model for the next iteration was made using 70% of the particles based on the best correlation during the alignment. For the finer step of refinement, a mask was used to restrict the alignment to an area covering 3 of the 8.3nm repeats.

1026 1026 249.66 90 90 90 P1