|Entry||Database: EMDB / ID: EMD-0770|
|Title||H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA, Class1|
|Sample||H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA, Class1|
|Function / homology|
Function and homology information
negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / telomere capping / negative regulation of tumor necrosis factor-mediated signaling pathway / interleukin-7-mediated signaling pathway / innate immune response in mucosa / DNA-templated transcription, initiation / telomere organization / DNA replication-dependent nucleosome assembly ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / telomere capping / negative regulation of tumor necrosis factor-mediated signaling pathway / interleukin-7-mediated signaling pathway / innate immune response in mucosa / DNA-templated transcription, initiation / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / chromatin silencing at rDNA / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / nuclear chromosome / regulation of gene silencing / regulation of megakaryocyte differentiation / protein heterotetramerization / nucleosome assembly / nucleosome / lipopolysaccharide binding / double-strand break repair via nonhomologous end joining / chromatin organization / nuclear chromosome, telomeric region / antibacterial humoral response / killing of cells of other organism / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / blood coagulation / cadherin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / negative regulation of cell population proliferation / nuclear chromatin / protein domain specific binding / cellular protein metabolic process / protein heterodimerization activity / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / nucleoplasm / extracellular region / nucleus / cytosol
Histone H3/CENP-A / Histone H2A, C-terminal domain / Histone H4 / Histone H2B / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / Histone H4, conserved site / Histone H2A / CENP-T/Histone H4, histone fold / Histone H2A conserved site
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 12.3 Å|
|Authors||Takizawa Y / Ho C-H / Tachiwana H / Ohi M / Wolf M / Kurumizaka H|
|Funding support|| Japan, 6 items |
|Citation||Journal: Structure / Year: 2019|
Title: Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.
Authors: Yoshimasa Takizawa / Cheng-Han Ho / Hiroaki Tachiwana / Hideyuki Matsunami / Wataru Kobayashi / Midori Suzuki / Yasuhiro Arimura / Tetsuya Hori / Tatsuo Fukagawa / Melanie D Ohi / Matthias Wolf / Hitoshi Kurumizaka /
Abstract: The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric ...The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric chromatin. However, little is known about how the CENP-A nucleosome affects the architecture of centromeric chromatin. In this study, we reconstituted tri-nucleosomes mimicking a centromeric nucleosome arrangement containing the CENP-A nucleosome, and determined their 3D structures by cryoelectron microscopy. The H3-CENP-A-H3 tri-nucleosomes adopt an untwisted architecture, with an outward-facing linker DNA path between nucleosomes. This is distinct from the H3-H3-H3 tri-nucleosome architecture, with an inward-facing DNA path. Intriguingly, the untwisted architecture may allow the CENP-A nucleosome to be exposed to the solvent in the condensed chromatin model. These results provide a structural basis for understanding the 3D configuration of CENP-A-containing chromatin, and may explain how centromeric proteins can specifically target the CENP-A nucleosomes buried in robust amounts of H3 nucleosomes in centromeres.
|Validation Report||PDB-ID: 6l4a|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0770.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.4 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA, Class1
|Entire||Name: H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA, Class1|
Number of components: 1
-Component #1: protein, H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA...
|Protein||Name: H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA, Class1|
Recombinant expression: No
|Mass||Theoretical: 600 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.03 mg/mL / pH: 7.8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 80 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON III (4k x 4k)|
|Image acquisition||Number of digital images: 4512|
|Processing||Method: single particle reconstruction / Number of projections: 7312|
|3D reconstruction||Software: RELION / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body|
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