[English] 日本語
![](img/lk-miru.gif)
- EMDB-22793: Nucleosome isolated from interphase chromosome formed in Xenopus ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-22793 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) | |||||||||
![]() | Nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) | |||||||||
![]() |
| |||||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Arimura Y / Funabiki H | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 32.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.5 KB 16.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 62.3 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 515.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 515.3 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kbdC ![]() 7kbeC ![]() 7kbfC C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data size: 634.3 Data #1: oligo nucleosome fraction from the interphase chromosome in Xenopus egg extract lot1 [micrographs - multiframe]) |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: Nucleosome isolated from interphase chromosome formed in Xenopus...
File | emd_22793_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Nucleosome isolated from interphase chromosome formed in Xenopus...
File | emd_22793_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : nucleosome isolated from interphase chromosome formed in Xenopus ...
Entire | Name: nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) |
---|---|
Components |
|
-Supramolecule #1: nucleosome isolated from interphase chromosome formed in Xenopus ...
Supramolecule | Name: nucleosome isolated from interphase chromosome formed in Xenopus egg extract (oligo fraction) (unbiased reconstruction) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
---|---|
Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 Component:
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 33.11 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |