2024-04-03 REL PDBe PDBe PDBe 2023-09-20 2024-03-13 2024-03-13 2024-04-03 Austrian Science Fund P33367 Austria Austrian Science Fund E435 Austria Chan Zuckerberg Initiative DAF2021-234754 United States European Research Council (ERC) 724373 European Union Cryo-electron tomogram of lift-out lamella from cell-derived extracellular matrix (example 5) Zens B Faessler F Hansen J Hauschild R Datler J Hodirnau V-V Zheden V Alanko J Sixt MK Schur FKM Extracellular matrix, cell-derived matrix, collagen, PROTEIN FIBRIL Zens B Fassler F Hansen JM Hauschild R Datler J Hodirnau VV Zheden V Alanko J Sixt M Schur FKM Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. J.Cell Biol. US 223 2024 38506714 doi:10.1083/jcb.202309125 1540-8140 2019 JCLBA3 EMD-18490 other EM volume EMD-18491 other EM volume EMD-18492 other EM volume EMD-18493 other EM volume Cryo-lamella prepared by lift-out cryo-FIB milling of cell-derived matrix from human telomerase-immortalized foreskin fibroblasts (TIFFs). Cryo-lamella prepared by lift-out cryo-FIB milling of cell-derived matrix from human telomerase-immortalized foreskin fibroblasts (TIFFs). 0
Cell-derived matrix was generated by growing TIFF cells on EM grids over 14 days of growth time.
Homo sapiens Skin Foreskin tomography cell 7.4 10.0 Dextran
10% Dextran in 0.1M Phosphate Buffer, pH 7.4
 Quantifoil R2/2 GOLD 200 CARBON HOLEY GLOW DISCHARGE AIR
ELMO Glow Discharge unit
 NITROGEN
Cell-derived matrix obtained from TIFF-cells.
OTHER
High pressure freezing carriers were 3.0mm in diameter and 0.5mm thick. One carrier was flat, the second carrier had a central cavity of 2.0mm diameter and 0.02mm depth. Carriers were coated in 1-hexadecene prior to high pressure freezing.. The value given for _em_high_pressure_freezing.instrument is Bal-tec HPM010. This is not in a list of allowed values {'BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM PACT2', 'LEICA EM HPM100', 'OTHER'} so OTHER is written into the XML file.
 10% Dextran (high MW) OTHER OTHER 30 0.03 3600 80 1000 250
A block of sample was extracted from the sample bulk by cryo-lift out FIB milling, with a thickness of 5000-8000nm. It was attached to a second grid, where it was then milled down to 200-250nm thickness step by step. Lamellae were milled in consecutive steps with 1nA (down to 3000nm thickness), 0.5nA (2000nm thickness), 0.1nA (1000nm), 50pA (500nm) and 30pA (200nm). See associated publication for details.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos II. 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 50.0 8.0 8.0 42000.0 42000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 83.0 GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 0.5 2.137 1 BACK PROJECTION
Reconstructed with AreTomo (version 1.3.4., Feb22) and processed with IsoNet (version 0.2).
61 emd_18494.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 510 720 250 0 0 0 510 720 250 8718.96 12309.12 4274.0 90.0 90.0 90.0 X Y Z -6.291202 4.457733 -0.46493977 0.29180554 17.096 17.096 17.096 AUTHOR Tomogram acquired on cryo-lift-out lamella of cell-derived matrix showing intra- and extracellular granular structures.