Cryo electron tomography data presented in Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites

REL 2025-10-21 2026-04-20 2026-04-20 Cryo electron tomography data presented in Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites 0000-0003-1905-0342 Giulia Zanetti The Francis Crick Institute The Crick Institute, 1 Brill Place, London United Kingdom NW1 1BF 0000-0003-1905-0342 Giulia Zanetti Institute of Structural and Molecular Biology, Birkbeck, University of London London United Kingdom WC1E 7HX Downes K Zanetti G European Research Council (ERC) ERC-StG-2019 grant 852915 United Kingdom 637.7 10.6019/EMPIAR-13270 EMDB cell EMD-56963 EMD-56606 EMD-56951 Downes K Flood J Nans A Van der Verren S Audhya A Zanetti G Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites bioRxiv United Kingdom 2025 English 10.1101/2025.07.29.667472

This deposition contains all the raw tilt series (frames + mdocs), reconstructed tomograms, membrane segmentations and ribosome coordinates used and presented in the associated paper.

Denoised tomograms containing COPII /data/ERES_Paper/denoised reconstructed volumes MRC MRC 63 42 1 42 16 BIT FLOAT 896 10.0 896 10.0

The 63 tilt series containing regions of interest were processed following the WarpTools pipeline, including motion correction, CTF and defocus handedness estimation (https://warpem.github.io/warp/). Tilt series were aligned using the WarpTools etomo patch tracking wrapper. Bad tilts were manually removed, and poorly aligned tilt series were manually improved with etomo. CTF-corrected tomograms were reconstructed at a pixel size of 10 Å and used to pick ribosomes for further improvement of alignments with Warp/M. Cryocare was used to denoise the tomograms.

data/ERES_Paper/predictions Membranes were segmented using membrain-seg v2. data/ERES_Paper/frames MRC Raw frames for the COPII containing tomograms /data/ERES_Paper/frames micrographs - multiframe MRC MRC 63 4 1 4 32 BIT FLOAT 3710 2.24 3838 2.24

Raw frames of the 63 COPII containing tilt series. Each tilt series contains 42 tilts. Also included is the star file for the ribosome picking which yielded a 15A ribosome map that was further used to improve tilt series alignments for tomogram reconstruction via the Warp/M pipeline.

data/ERES_Paper/frames/*.mrc data/ERES_Paper/job001/run_data.star data/ERES_Paper/job001 mdocs /data/ERES_Paper/mdoc_correctedFractions tilt series MRC MRC 63 4 1 4 BIT 3710 2.24 3838 2.24

mdocs for the 63 COPII containing tomograms.