Fibroblast nucleus sub-volume.

2023-12-13 REL PDBe PDBe PDBe 2022-05-30 2022-07-06 2022-07-06 2023-12-13 Israel Science Foundation 1696/18 Israel Fibroblast nucleus sub-volume. Sedat J McDonald A Elbaum M nucleus, chromatin, STEM, DNA Sedat J McDonald A Cang H Lucas J Arigovindan M Kam Z Murre C Elbaum M A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence. Proc.Natl.Acad.Sci.USA US 119 e2119101119 e2119101119 2022 35749363 doi:10.1073/pnas.2119101119 1091-6490 0040 PNASA6 EMD-14924 other EM volume

sub-volume used for stereo movie (RASP) in publication

WI-38 fibroblast cell WI-38 fibroblast cell 0

cells cultured directly on gold EM grid

Homo sapiens lung cell culture tomography cell 7.4

Minimal Essential Medium (Gibco) supplemented with 15% fetal calf serum, L-glutamine, and penicillin/streptomycin.

ETHANE LEICA EM GP

WI-38 embryonic lung fibroblast cells (obtained from Coriell Institute) were cultured directly on gold EM grids and imaged intact by cryo-STEM tomography (CSTET).

obtained from L Duchesne (https://doi.org/10.1021/la802876u ) 10 NO SECTIONING FEI TECNAI F20 SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 200 20.0 2.0 0.0 0.0 GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN

STEM data collection in BF mode.

NanoProbe STEM acquisition.

OTHER 2048 2048 1 61 12.6 3.8

Cryo-STEM tilt series

Gatan STEM BF/ADF detector

BACK PROJECTION TOMO3D PRIISM/IVE

The original alignment was done using etomo (IMOD), and then optimized using tomoalign as a "thin" specimen. A new aligned stack (.ali) was produced using tomowarpalign (tomoalign) and reconstructed by SIRT using tomo3d. The reconstruction was then binned (by 2) and processed by 3D deconvolution as described in Waugh et al (doi:10.1073/pnas.2000700117) with smoothing parameter 0.1.

56 emd_15057.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 570 374 100 396 650 261 570 374 100 19095.0 12529.0 3350.0 90.0 90.0 90.0 X Y Z 1500.0 3367.148200000000088 1613.101699999999937 130.039950000000005 33.5 33.5 33.5 AUTHOR ::::EMDATABANK.org::::EMD-15057:::: sub-volume of EMD-14924. corresponds to Supplementary Movie S2.