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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23630 | |||||||||
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Title | H2A.Z Dodecanucleosome 30 nm Fiber | |||||||||
![]() | Chromatin fiber containing mouse histone variant H2A.Z | |||||||||
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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 | ![]() ![]() | |||||||||
![]() | Lewis T / Sokolova V / Ng H / Tan D | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.5 KB 22.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 73.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 326.8 KB | Display | ![]() |
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Full document | ![]() | 326.4 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Chromatin fiber containing mouse histone variant H2A.Z | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.079 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : In vitro reconstituted 12x167 bp chromatin
+Supramolecule #1: In vitro reconstituted 12x167 bp chromatin
+Supramolecule #2: Histone H2A.Z
+Supramolecule #3: Histone H2B
+Supramolecule #4: 12 tandem repeats of 167 bp of 601 Windom nucleosome-positioning ...
+Supramolecule #5: Histone H3
+Supramolecule #6: Histone H4
+Macromolecule #1: Histone H2A.Z
+Macromolecule #2: Histone H2B
+Macromolecule #3: Histone H3
+Macromolecule #4: Histone H4
+Macromolecule #5: 12 tandem repeats of 167 bp of 601 Windom nucleosome-positioning ...
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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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: Sample was absorbed on the grid for thirty seconds, then blotted for five seconds with a blot force zero before plunge freezing.. | ||||||||||||
Details | The sample is crosslinked with 0.1% glutaraldehyde |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / 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: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 5 / Number real images: 14425 / Average electron dose: 31.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |