2019-02-13 REL PDBe PDBe PDBe 2018-12-20 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 map of volume also used in the work cited.

EMD-4486 other EM volume

EMD-4486 contains map of volume also used in the work cited.

EMD-4484 other EM volume

EMD-4484 contains map of volume also used in the work cited.

EMD-4490 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

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 R2/2 GOLD 200 CARBON HOLEY ETHANE HOMEMADE PLUNGER

Grids were manually backside blotted using Whatman filter paper No. 1 and vitrified using a manual plunger..

HeLa cells were grown for 24 h on 200 mesh gold grids with a holey carbon film R2/2 (Quantifoil) in 6-well plates and transfected with 2000 ng hBax-C3-EGFP plasmid in presence of Q-VD-OPh. 16 hours after transfection, cells were stained with MitoTracker Deep Red, grids were manually backside blotted using Whatman filter paper No. 1 and vitrified using a manual plunger.

OTHER OTHER 30 1 10800 83 1000 200

Cells were cryo-FIB milled to prepare lamellae using a Scios DualBeam FIB/SEM (FEI) equipped with a Quorum cryo-stage (PP3010T), following the protocol described in Schaffer et al. (2015). In brief, grids were coated with an organic Pt compound using the gas injection system for either 8 s at 12 mm working distance or 30 s at 13 mm working distance from a stage tilt of 25 degrees. The stage was then tilted so that the grid was at a 10 degree angle towards the ion beam for all subsequent steps. The electron beam was used at 13 pA and 5-10 kV to locate cells, 2 kV for subsequent imaging. The ion beam was used at 30 kV and 10 pA for imaging. Rough milling was performed at 30 kV ion beam voltage, and subsequently the current was reduced from 0.5 nA to 0.3 nA until a lamella thickness of 5 um was reached, and further to 0.1 nA until 1 um lamella thickness. Fine milling to a final lamella thickness of approximately 200 nm was performed either at 30 kV and 30 pA, or 16 kV and 11 pA ion beam setting.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios DualBeam FIB/SEM. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.

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 either 190.9 or 99.4 nm. Intermediate magnification maps of lamella 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

10 iterations

83