|Entry||Database: EMDB / ID: EMD-0768|
|Title||H3-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA|
|Sample||H3-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA|
|Function / homology|
Function and homology information
condensed chromosome inner kinetochore / protein localization to chromosome, centromeric region / kinetochore assembly / nuclear pericentric heterochromatin / condensed nuclear chromosome kinetochore / negative regulation of megakaryocyte differentiation / condensed nuclear chromosome, centromeric region / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / DNA replication-independent nucleosome assembly ...condensed chromosome inner kinetochore / protein localization to chromosome, centromeric region / kinetochore assembly / nuclear pericentric heterochromatin / condensed nuclear chromosome kinetochore / negative regulation of megakaryocyte differentiation / condensed nuclear chromosome, centromeric region / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / DNA replication-independent nucleosome assembly / telomere capping / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / interleukin-7-mediated signaling pathway / mitotic cytokinesis / 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 / chromatin organization / double-strand break repair via nonhomologous end joining / 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 / chromatin binding / cellular protein metabolic process / viral process / protein heterodimerization activity / cell / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / nucleoplasm / extracellular region / nucleus / cytosol
Histone-fold / Histone H4 / Histone H4, conserved site / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor (TAF) / Histone H2A / Histone H2B / Histone H2A/H2B/H3 / Histone H3/CENP-A
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4 / Histone H3.1
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 18.7 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: 6l49|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0768.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-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA
|Entire||Name: H3-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA|
Number of components: 1
-Component #1: protein, H3-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA
|Protein||Name: H3-CENP-A-H3 tri-nucleosome with the 22 base-pair linker DNA|
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: 25 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 II (4k x 4k)|
|Image acquisition||Number of digital images: 4515|
|Processing||Method: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 4999|
|3D reconstruction||Software: RELION / Resolution: 18.7 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi