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Yorodumi- EMDB-22796: Alpha2-macroglobulin family protein isolated from metaphase chrom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22796 | |||||||||
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Title | Alpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract | |||||||||
Map data | Alpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract | |||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Arimura Y / Funabiki H | |||||||||
Funding support | United States, Japan, 2 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural features of nucleosomes in interphase and metaphase chromosomes. Authors: Yasuhiro Arimura / Rochelle M Shih / Ruby Froom / Hironori Funabiki / Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo- ...Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22796.map.gz | 61.7 MB | EMDB map data format | |
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Header (meta data) | emd-22796-v30.xml emd-22796.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22796_fsc.xml | 11.2 KB | Display | FSC data file |
Images | emd_22796.png | 114.3 KB | ||
Masks | emd_22796_msk_1.map | 125 MB | Mask map | |
Others | emd_22796_half_map_1.map.gz emd_22796_half_map_2.map.gz | 115.6 MB 115.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22796 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22796 | HTTPS FTP |
-Validation report
Summary document | emd_22796_validation.pdf.gz | 550.1 KB | Display | EMDB validaton report |
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Full document | emd_22796_full_validation.pdf.gz | 549.6 KB | Display | |
Data in XML | emd_22796_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_22796_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22796 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22796 | HTTPS FTP |
-Related structure data
Related structure data | 7kbdC 7kbeC 7kbfC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10691 (Title: Oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract (lot1) Data size: 1.3 TB Data #1: oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract lot1 [micrographs - multiframe] Data #2: oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract lot1 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22796.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Alpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22796_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Alpha2-macroglobulin family protein isolated from metaphase chromosome formed...
File | emd_22796_half_map_1.map | ||||||||||||
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Annotation | Alpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Alpha2-macroglobulin family protein isolated from metaphase chromosome formed...
File | emd_22796_half_map_2.map | ||||||||||||
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Annotation | Alpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : nucleosome isolated from metaphase chromosome formed in Xenopus e...
Entire | Name: nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) |
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Components |
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-Supramolecule #1: nucleosome isolated from metaphase chromosome formed in Xenopus e...
Supramolecule | Name: nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 38.34 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 35.27 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |