+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15061 | |||||||||
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Title | Fibroblast nucleus sub-volume. | |||||||||
Map data | sub-volume of EMD-14924. corresponds to Supplementary Movie S6. | |||||||||
Sample |
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Keywords | nucleus / chromatin / STEM / DNA | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Sedat J / McDonald A / Elbaum M | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence. Authors: John Sedat / Angus McDonald / Hu Cang / Joseph Lucas / Muthuvel Arigovindan / Zvi Kam / Cornelis Murre / Michael Elbaum / Abstract: Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome ...Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman , 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15061.map.gz | 44.2 MB | EMDB map data format | |
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Header (meta data) | emd-15061-v30.xml emd-15061.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_15061.png | 118.9 KB | ||
Filedesc metadata | emd-15061.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15061 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15061 | HTTPS FTP |
-Validation report
Summary document | emd_15061_validation.pdf.gz | 440.8 KB | Display | EMDB validaton report |
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Full document | emd_15061_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | emd_15061_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_15061_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15061 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15061 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15061.map.gz / Format: CCP4 / Size: 63.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sub-volume of EMD-14924. corresponds to Supplementary Movie S6. | ||||||||||||||||||||
Voxel size | X=Y=Z: 33.5 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : WI-38 fibroblast cell
Entire | Name: WI-38 fibroblast cell |
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Components |
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-Supramolecule #1: WI-38 fibroblast cell
Supramolecule | Name: WI-38 fibroblast cell / type: cell / ID: 1 / Parent: 0 / Details: cells cultured directly on gold EM grid |
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Source (natural) | Organism: Homo sapiens (human) / Organ: lung / Tissue: cell culture |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: Minimal Essential Medium (Gibco) supplemented with 15% fetal calf serum, L-glutamine, and penicillin/streptomycin. |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
Details | 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). |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: obtained from L Duchesne (https://doi.org/10.1021/la802876u ) Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Specialist optics | Details: STEM data collection in BF mode. |
Details | NanoProbe STEM acquisition. |
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 61 / Average exposure time: 12.6 sec. / Average electron dose: 3.8 e/Å2 / Details: Cryo-STEM tilt series |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Gatan STEM BF/ADF detector |
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Final reconstruction | Algorithm: BACK PROJECTION / Software: (Name: TOMO3D, PRIISM/IVE) / Number images used: 56 |