2019-02-13 REL PDBe PDBe PDBe 2018-12-19 2019-02-13 2019-02-13 2019-02-13 Ader NR Hoffmann PC Ganeva I Borgeaud AC Wang C Youle RJ Kukulski W Ader NR Hoffmann PC Ganeva I Borgeaud AC Wang C Youle RJ Kukulski W Elife US 8 2019 30714902 doi:10.7554/eLife.40712 2050-084X EMD-4483 other EM volume

EMD-4483 contains another volume from the cited work.

EMD-4484 other EM volume

EMD-4484 contains another volume from the cited work.

EMD-4486 associated EM volume HeLa (homo sapiens) HeLa (homo sapiens) 0

Cryofixation of cell was performed 16 h after transfection of GFP-Bax plasmid.

Homo sapiens tomography cell 7.4 PBS

DMEM, high glucose, GlutaMAX, pyruvate (Thermo 31996) medium supplemented with 10% heat-inactivated FBS (Gibco 10270), 10 mM HEPES, and 1x NEAA (Thermo 11140)

Quantifoil R3.5/1 COPPER CARBON HOLEY PLASMA CLEANING NITROGEN

high pressure frozen.

OTHER

HeLa cells were grown for 24 h in 6-well plates, transfected with 2000 ng hBax-C3-EGFP plasmid and incubated with Q-VD-OPh for 16 h, then trypsinized and pelleted. Immediately before trypsinizing, cells were stained with MitoTracker Deep Red. Pellets were maintained at 37 degrees C while they were mixed 1:1 with 40% Dextran (Sigma) in PBS, pipetted into the 0.2 mm recess of gold-coated copper carriers, covered with the flat side of Aluminum carriers B and high-pressure frozen with a Leica HPM100 (Leica Microsystems).. The value given for _emd_high_pressure_freezing.instrument is Leica EM HP100. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.

40% Dextran Leica UC6/FC6 123 100

100 nm thick vitreous sections were produced at -150 degrees C in a UC6/FC6 cryo-ultramicrotome (Leica Microsystems) using cryotrim 25 and a 35 degree cryo immuno knives (Diatome). The sections were attached using a Crion antistatic device (Leica Microsystems) to EM grids (R3.5/1, copper, Quantifoil) that were plasma cleaned and had 100 nm TetraSpeck beads (Invitrogen) diluted 1:50 in PBS adhered to them.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 5.0 5.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20

Montaged images of the entire grid were acquired at low magnification at pixel size of 182.3 nm. Intermediate magnification maps of grid squares with vitreous sections were acquired at pixel size 5.5 nm.

GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1.1

Electron cryo-tomographic tilt-series were collected on a Titan Krios (FEI) operated at 300 kV using a Quantum energy filter (slit width 20 eV) and a K2 direct electron detector (Gatan) in counting mode at a pixel size of 3.7 angstroms and at a dose rate of ~ 2-4 e-/pixel/second on the detector, dependent on sample thickness. Tilt-series were acquired between +/- 60 degrees starting from 0 degrees with 1 degrees increment using SerialEM (Mastronarde, 2005) following a grouped dose-symmetric acquisition with a group size of 4 (Bharat et al., 2018; Hagen et al., 2017), and at -5 um defocus. A dose of approximately 1.0 to 1.2 e-/square angstroms was applied per image of the tilt-series.

1 SIMULTANEOUS ITERATIVE (SIRT) eTomo 4.10.20

NUmber of tilted images used in for this volume is approximate.

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