2026-03-11 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-10-21 2026-03-11 2026-03-11 2026-03-11 Wellcome Trust 225902/Z/22/Z United Kingdom Wellcome Trust 220526/Z/20/Z United Kingdom Wellcome Trust 226810/Z/22/Z United Kingdom Glynn C Smith JLR synapse, vesicles, cell adhesion molecules, CELL ADHESION Glynn C Smith JLR Case M Csondor R Katsini A Sanita ME Glen TS Pennington A Grange M Cell Rep Methods 5 101080 2025 40527314 doi:10.1016/j.jsb.2016.06.024 2667-2375 EMDB EMD-55442 associated EM volume mouse hippocampal CA1 stratum radiatum mouse hippocampal CA1 stratum radiatum 0

synapse from hippocampal layer CA1-sr from the right hemisphere of a 172 day old female mouse

Mus musculus C57BL/6 brain tomography tissue 7.4

92 mM NMDG, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na-ascorbate, 3 mM Na-pyruvate, 0.5 mM CaCl2 2H2O, and 10 mM MgSO4 7H2O

COPPER NITROGEN

Leica EM Ice HPF.

synapse from the right hemisphere of a 172 day old female mouse hippocampus CA1 stratum radiatum.

OTHER

3 mm x 0.5 mm gold plated copper high pressure freezing carriers with 0.1 mm recess. Carriers were coated with hexadecene > 45 minutes prior to use.. The value given for _em_high_pressure_freezing.instrument is Leica EM Ice. This is not in a list of allowed values {'LEICA EM PACT2', 'LEICA EM PACT', 'OTHER', 'BAL-TEC HPM 010', 'LEICA EM HPM100', 'EMS-002 RAPID IMMERSION FREEZER'} so OTHER is written into the XML file.

10% dextran 10% sucrose in NMDG buffer pH 7.4 OTHER OTHER 30 0.001 3600 100 100000 177

Lamella were prepared starting from 100 micron thick tissue sections in high pressure freezing carriers using the serial lift-out method on a Helios Hydra plasma FIB. Milling and serial sectioning was carried out using xenon gas and currents ranging from 1 nA to 60 nA depending on step. Thinning was then carried out on an Arctis pFIB starting with xenon gas and progressively lower currents from 4 nA to 100 pA. Once the lamella reached 400-600 nm thickness, argon was used for polishing with currents of 60 pA followed by 20 pA to the final thickness.. The value given for _em_focused_ion_beam.instrument is helios hydra and Arctis. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 3.0 5.0 64000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 130.0 1

preprocessing carried out in warp. reconstruction carried out in aretomo2 with SART reconstruction at bin8.

ALGEBRAIC (ARTS) Warp aretomo2, not warp 41 Warp 1.0.9 PHASE FLIPPING ONLY