|Entry||Database: EMDB / ID: EMD-10158|
|Title||Class 1B : CENP-A nucleosome|
|Sample||Class 1B : CENP-A nucleosome|
|Function / homology|
Function and homology information
condensed chromosome inner kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / pericentric heterochromatin => GO:0005721 / condensed nuclear chromosome kinetochore / condensed chromosome, centromeric region => GO:0000779 / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / chromosome, centromeric region ...condensed chromosome inner kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / pericentric heterochromatin => GO:0005721 / condensed nuclear chromosome kinetochore / condensed chromosome, centromeric region => GO:0000779 / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / chromosome, centromeric region / DNA replication-independent nucleosome assembly / telomere capping / mitotic cytokinesis / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / double-strand break repair via nonhomologous end joining / chromatin organization / chromosome, telomeric region => GO:0000781 / antibacterial humoral response / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / protein heterodimerization activity / defense response to Gram-positive bacterium / chromatin => GO:0000785 / protein domain specific binding / chromatin binding / cellular protein metabolic process / viral process / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol
Histone H4 / Histone H2A / Histone H4, conserved site / Histone H2A, C-terminal domain / Histone H2A conserved site / TATA box binding protein associated factor (TAF) / CENP-T/Histone H4, histone fold / Histone H2B / Histone H2A/H2B/H3 / Histone H3/CENP-A / Histone-fold
Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H2A type 2-A
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.4 Å|
|Authors||Ali-Ahmad A / Bilokapic S / Halic M / Sekulic N|
|Funding support|| Norway, Germany, 2 items |
|Citation||Journal: EMBO Rep / Year: 2019|
Title: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Authors: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić /
Abstract: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_10158.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.06 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Class 1B : CENP-A nucleosome
|Entire||Name: Class 1B : CENP-A nucleosome / Number of components: 1|
-Component #1: protein, Class 1B : CENP-A nucleosome
|Protein||Name: Class 1B : CENP-A nucleosome / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1.2 mg/mL / pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 47000|
|3D reconstruction||Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF|
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