+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23630 | |||||||||
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Title | H2A.Z Dodecanucleosome 30 nm Fiber | |||||||||
Map data | Chromatin fiber containing mouse histone variant H2A.Z | |||||||||
Sample |
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Function / homology | Function and homology information Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / multicellular organism development ...Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / multicellular organism development / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / cellular response to estradiol stimulus / euchromatin / chromatin DNA binding / structural constituent of chromatin / cellular response to insulin stimulus / nucleosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Lewis T / Sokolova V / Ng H / Tan D | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23630.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-23630-v30.xml emd-23630.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23630_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_23630.png | 73.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23630 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23630 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23630.map.gz / Format: CCP4 / Size: 58 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Chromatin fiber containing mouse histone variant H2A.Z | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
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 |