REL 2022-08-09 2022-09-26 2022-09-26 0000-0002-5297-9156 Cristina Capitanio Max Planck Institute of Biochemistry, Martinsried Am Klopferspitz 18 Martinsried, Planegg Bayern Germany 82152 0000-0002-6559-7261 Florian Wilfling Max Planck Institute of Biophysics Max-von-Laue Str. 3 Frankfurt am Main Germany 60438 0000-0001-8154-8809 Wolfgang Baumeister Max Planck Institute of Biochemistry Am Klopferspitz 18 Martinsried Germany 82152 0000-0002-3083-1126 Brenda A Schulman Max Planck Institute of Biochemistry Am Klopferspitz 18 Martinsried Germany 82152 0000-0001-8289-9133 Philipp S Erdmann Human Technopole Viale Rita Levi-Montalcini, 1 Milan Italy 20157 Bieber A Capitanio C Erdmann PS Schulman BA Baumeister W Wilfling F 249.0 10.6019/EMPIAR-11166 EMDB cell EMD-15526 EMD-15545 EMD-15546 EMD-15547 EMD-15548 EMD-15549 Bieber A Capitanio C Erdmann PS Fiedler F Beck F Lee CW Li D Hummer G Schulman BA Baumeister W Wilfling F King J Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A 39 119 2022 English 10.1073/pnas.2209823119 36122245 Aligned and sorted tilt series of autophagic structures in S. cerevisiae, not dose-filtered, with corresponding mdocs. /data tilt series MRC MRC 84 10 UNSIGNED 32 BIT INTEGER 3712 3.52 3712 3.52

84 tilt series of autophagic structures captured in situ in S. cerevisiae. The tilt series were recorded on cryo-FIB-milled lamellae at positions corresponding to fluorescence signal (eGFP-Atg8 or mCherry-Atg8 + eGFP-Ede1). Data collected on a Titan Krios (300 kV) equipped with Gatan K2 Summit Camera and Gatan Quantum K2 energy filter at a magnification of 42000 X. Tilt series were acquired in SerialEM (v 3.9.0) following a dose-symmetric scheme, 2 degrees per tilt step, +/- 60 degrees around a starting angle of either + or -10 degrees, to compensate for the pre-tilt of the lamellae. Exposure per tilt image is 2.0 electrons per angstrom squared. Original frames were aligned with Motioncorr2 (v1.4.0). Here we provide aligned and sorted tilt series stacks, not dose-filtered. Mdocs associated to each tilt series are in the mdocs folder. The file TS_descriptions.csv specifies the yeast strain for each tilt series and the type of autophagic structure in it (phagophore, autophagosome or autophagsome fusion with the vacuole). The following tilt series correspond to specific EMDB entries: EMD-15526: TS_073 EMD-15545: TS_044 EMD-15546: TS_003 EMD-15547: TS_047 EMD-15548: TS_071 EMD-15549: TS_057