2026-04-15 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2026-02-06 2026-04-15 2026-04-15 2026-04-15 European Research Council (ERC) ERC-StG-2019 grant 852915 European Union Cryo-tomogram of COPI and COPII vesicles and buds from FIB-milled RPE-1 cells. Downes KW Zanetti G Nans A Intracellular Coat, Human, COPII, COPI, TRANSPORT PROTEIN Downes KW Flood J Nans A VanderVerren S Audhya A Zanetti G Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites biorxiv US doi:10.1101/2025.07.29.667472 2692-8205 0353 EMDB EMD-56606 associated EM volume COPI and COPII coats in Halo_Sec23A RPE-1 cells. COPI and COPII coats in Halo_Sec23A RPE-1 cells. 0
Halo tag added to endogenous site of Sec23A in RPE-1 cells, used to target lamella production by FIB-milling and tomograms positioning.
Homo sapiens Halo_Sec23A RPE-1 ERES tomography threeDArray 7.4 1.0 DMEM/F12 DMEM/F12, 10% FBS, L-glutamine, 1% Pen/Strep NONE Oregon Green-HaloTag Ligand
Cells stained with 1 uL/mL Oregon Green-HaloTag Ligand
 Quantifoil R2/2 MOLYBDENUM 200 CARBON HOLEY PLASMA CLEANING
Tergeo-EM (PIE scientific)
 ETHANE 70 310 LEICA EM GP OTHER OTHER 30 1 3000 81 800 160
Lamella positions, eucentric height and milling angles were automatically calculated in AutoTEM 2.4 (Thermo Fisher). Final lamella placement was guided by the site of interest/fiducial pair that was added in MAPS and identified in the FIB image. The length and position of the lamella was optimized for each cell. Lamellae were produced using a Gallium beam, operating at 30 kV, in a stepwise manner starting at a beam current of 1.0 nA for rough milling and decreasing to 0.5 nA and 0.3 nA for medium and fine milling. Thinning was then performed in two stages with a beam current of first 50 pA, and then 30 pA. Target milling angles ranged from 9 to 15 and the target lamella thickness was set between 150 and 250 nm.. The value given for _em_focused_ion_beam.instrument is Aquilos2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 8.0 8.0 GATAN K2 BASE (4k x 4k) 3.5 1 Warp 42 Warp
WARP pipeline
PHASE FLIPPING AND AMPLITUDE CORRECTION emd_56606.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 896 896 448 3 -4 1 896 896 448 8960.0 8960.0 4480.0 90.0 90.0 90.0 X Y Z -0.16640995 0.24021563 -0.00004516539 0.0049080825 10.0 10.0 10.0 AUTHOR Tomogram showing COPI and COPII vesicles and buds derived from plunge frozen, FIB-milled, Halo_Sec23A RPE-1 cells.