2021-12-15 REL PDBe PDBe PDBe 2021-03-19 2021-12-08 2021-12-08 2021-12-15 Medical Research Council (MRC, United Kingdom) MRC_UP_A025_1011 United Kingdom Wellcome Trust WT210711 United Kingdom In situ subtomogram average of 13 protofilament microtubule from Mus musculus DRG axons Foster HE Ventura Santos C Carter AP Foster HE Ventura Santos C Carter AP A cryo-ET survey of microtubules and intracellular compartments in mammalian axons. J.Cell Biol. US 221 2022 34878519 doi:10.1083/jcb.202103154 1540-8140 2019 JCLBA3 Foster HE Carter AP A cryo-ET survey of intracellular compartments within mammalian axons Biorxiv US 2021 doi:10.1101/2021.03.29.437454 EMD-12639 associated EM volume In situ subtomogram average of 13 protofilament microtubule from Mus musculus DRG axons In situ subtomogram average of 13 protofilament microtubule from Mus musculus DRG axons 0 1 Mus musculus Neurons Dorsal root ganglion microtubule cytoskeleton axoplasm subtomogramAveraging cell 7.4 Quantifoil R3.5/1 GOLD 200 CARBON CONTINUOUS PLASMA CLEANING OTHER
Grids were additionally coated in 0.1mg/mL poly-L-lysine then 0.01mg/mL laminin before cell plating
 ETHANE 100 310 FEI VITROBOT MARK IV
Manual blot for 3 s before plunging.
Microtubules in axons of adult DRG neurons grown for 7 days in vitro
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 3.0 5.0 53000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1-10 1.7 1.85
61 images per tilt series with 112.85 e/A2 total dose.
 1 C1 BACK PROJECTION 12.0 FSC 0.143 CUT-OFF RELION 3.0 postprocess
Particles were aligned together at bin4. Half maps were generated at bin4 and independently aligned at bin2 and bin1.
64528 39 476268 average of all particles (tube-shape) Dynamo filament extraction IMOD 4.10.32 model Dynamo 1.1.333 particle position determination
Paths of microtubules were modelled in IMOD (version 4.10.32). After importing into Dynamo, initial particle positions were determined using the 'filamentWithTorsion' model workflow. Helical symmetry was applied at the particle level and subvolumes were extracted using subTOM.
 NOVACTF 1.0.0 IMOD 4.10.32
Defoci were estimated with CTFPLOTTER (IMOD version 4.10.32). CTF correction was done with novaCTF.
 OTHER
Alignment, classification and averaging was performed in subTOM (1.1.5)
 emd_12639.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 528.0 528.0 528.0 90.0 90.0 90.0 X Y Z -0.24335557 0.33154163 -0.00021993526 0.063600354 2.75 2.75 2.75 0.0719 AUTHOR microtubule structure from mouse DRG axons emd_12639_msk_1.map emd_12639_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 528.0 528.0 528.0 90.0 90.0 90.0 X Y Z -0.26428187 0.33655053 0.00010829941 0.0663164 2.75 2.75 2.75 AUTHOR emd_12639_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 528.0 528.0 528.0 90.0 90.0 90.0 X Y Z -0.26307026 0.3320153 0.000120509765 0.06462538 2.75 2.75 2.75 AUTHOR