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Yorodumi- EMDB-6846: Volta phase contrast cryotomogram of a cryosectioned prometaphase... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6846 | ||||||||||||||||||
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Title | Volta phase contrast cryotomogram of a cryosectioned prometaphase S. pombe cell, strain nda3-KM311 | ||||||||||||||||||
Map data | Volta phase contrast cryotomogram of a cryosectioned prometaphase S. pombe cell, strain nda3-KM311 | ||||||||||||||||||
Sample |
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Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||
Authors | Cai S / Chen C / Tan Z / Huang Y / Shi J / Gan L | ||||||||||||||||||
Funding support | Singapore, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Cryo-ET reveals the macromolecular reorganization of mitotic chromosomes in vivo. Authors: Shujun Cai / Chen Chen / Zhi Yang Tan / Yinyi Huang / Jian Shi / Lu Gan / Abstract: Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription. Here, we use cryo-electron ...Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription. Here, we use cryo-electron tomography (cryo-ET) to determine the 3D arrangement of nuclear macromolecular complexes, including nucleosomes, in frozen-hydrated cells. Using 3D classification analysis, we did not find evidence that nucleosomes resembling the crystal structure are abundant. This observation and those from other groups support the notion that a subset of fission yeast nucleosomes may be partially unwrapped in vivo. In both interphase and mitotic cells, there is also no evidence of monolithic structures the size of Hi-C domains. The chromatin is mingled with two features: pockets, which are positions free of macromolecular complexes; and "megacomplexes," which are multimegadalton globular complexes like preribosomes. Mitotic chromatin is more crowded than interphase chromatin in subtle ways. Nearest-neighbor distance analyses show that mitotic chromatin is more compacted at the oligonucleosome than the dinucleosome level. Like interphase, mitotic chromosomes contain megacomplexes and pockets. This uneven chromosome condensation helps explain a longstanding enigma of mitosis: a subset of genes is up-regulated. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6846.map.gz | 3.4 GB | EMDB map data format | |
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Header (meta data) | emd-6846-v30.xml emd-6846.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_6846.png | 212.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6846 | HTTPS FTP |
-Validation report
Summary document | emd_6846_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_6846_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_6846_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6846 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6846 | HTTPS FTP |
-Related structure data
EM raw data | EMPIAR-10125 (Title: Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo Data size: 35.1 Data #1: Tilt series of fission yeast cells and chromatin lysates in various cell cycle states [tilt series]) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6846.map.gz / Format: CCP4 / Size: 4.5 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Volta phase contrast cryotomogram of a cryosectioned prometaphase S. pombe cell, strain nda3-KM311 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : S. pombe cell, arrested in prometaphase
Entire | Name: S. pombe cell, arrested in prometaphase |
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Components |
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-Supramolecule #1: S. pombe cell, arrested in prometaphase
Supramolecule | Name: S. pombe cell, arrested in prometaphase / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) / Strain: nda3-KM311 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: yeast-extract supplemented |
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Grid | Model: C-flat-1/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
High pressure freezing | Instrument: OTHER Details: Self-pressurized freezing. The value given for _emd_high_pressure_freezing.instrument is Vitrobot cup. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS- ...Details: Self-pressurized freezing. The value given for _emd_high_pressure_freezing.instrument is Vitrobot cup. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file. |
Cryo protectant | 30% dextran |
Sectioning | Ultramicrotomy - Instrument: Leica UC7/FC7 / Ultramicrotomy - Temperature: 123 K / Ultramicrotomy - Final thickness: 100 nm |
Fiducial marker | Manufacturer: BBI / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 61 / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 30400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9) / Number images used: 61 |
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