[English] 日本語

- EMDB-23626: Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-23626 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z | |||||||||
![]() | cryo-EM map of nucleosome containing histone variant H2A.Z | |||||||||
![]() |
| |||||||||
Function / homology | ![]() Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / DNA Damage/Telomere Stress Induced Senescence / heterochromatin assembly => GO:0031507 / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / nucleosomal DNA binding ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / DNA Damage/Telomere Stress Induced Senescence / heterochromatin assembly => GO:0031507 / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / nucleosomal DNA binding / multicellular organism development / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Tan D / Lewis T | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural basis of chromatin regulation by histone variant H2A.Z. Authors: Tyler S Lewis / Vladyslava Sokolova / Harry Jung / Honkit Ng / Dongyan Tan / ![]() Abstract: The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an ...The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z's ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 26.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 26.7 KB 26.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.8 KB | Display | ![]() |
Images | ![]() | 199.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 336.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 336.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m1xMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cryo-EM map of nucleosome containing histone variant H2A.Z | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Nucleosome core particle containing variant H2A.Z and canonical c...
+Supramolecule #1: Nucleosome core particle containing variant H2A.Z and canonical c...
+Supramolecule #2: Histone H3
+Supramolecule #3: Histone H4
+Supramolecule #4: Histone variant H2A.Z
+Supramolecule #5: Histone H2B
+Supramolecule #6: DNA (136-MER)
+Supramolecule #7: DNA (136-MER)
+Macromolecule #1: DNA (136-MER)
+Macromolecule #2: DNA (136-MER)
+Macromolecule #3: Histone H3
+Macromolecule #4: Histone H4
+Macromolecule #5: Histone H2A.Z
+Macromolecule #6: Histone H2B 1.1
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4.5 seconds before plunging. | |||||||||||||||
Details | This sample was mono-disperse. |
-
Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 123811 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 1950 / Average exposure time: 60.0 sec. / Average electron dose: 33.0 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Initial model |
| ||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: rmsd | ||||||||||||||||||||||
Output model | ![]() PDB-7m1x: |