|Entry||Database: EMDB / ID: EMD-10156|
|Title||Class 2B : CENP-A nucleosome in complex with CENP-C central region|
|Sample||Class 2B : CENP-A nucleosome in complex with CENP-C central region:|
|Function / homology|
Function and homology information
monopolar spindle attachment to meiosis I kinetochore / centromeric DNA binding / condensed chromosome inner kinetochore / attachment of mitotic spindle microtubules to 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 ...monopolar spindle attachment to meiosis I kinetochore / centromeric DNA binding / condensed chromosome inner kinetochore / attachment of mitotic spindle microtubules to 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 / pericentric heterochromatin / chromosome, centromeric region / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / mitotic cytokinesis / telomere capping / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 / kinetochore / 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 / chromosome segregation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / midbody / mitotic cell cycle / double-strand break repair via nonhomologous end joining / chromatin organization / chromosome, telomeric region => GO:0000781 / antibacterial humoral response / nuclear body / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / protein heterodimerization activity / defense response to Gram-positive bacterium / cell division / chromatin => GO:0000785 / protein domain specific binding / cellular protein metabolic process / chromatin binding / 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 H2B / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Histone H4, conserved site / Mif2/CENP-C cupin domain ...Histone H4 / Histone H2B / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Histone H4, conserved site / Mif2/CENP-C cupin domain / Kinetochore assembly subunit CENP-C, N-terminal domain / Histone H3/CENP-A / Centromere protein C/Mif2/cnp3 / CENP-C, middle DNMT3B-binding domain / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold
Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Histone H2A type 2-A
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.7 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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_10156.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.3 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Class 2B : CENP-A nucleosome in complex with CENP-C central region
|Entire||Name: Class 2B : CENP-A nucleosome in complex with CENP-C central region|
Number of components: 2
-Component #1: protein, Class 2B : CENP-A nucleosome in complex with CENP-C cent...
|Protein||Name: Class 2B : CENP-A nucleosome in complex with CENP-C central region|
Recombinant expression: No
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
-Component #2: nucleic-acid, CENP-A nucleosome
|nucleic acid||Name: CENP-A nucleosome / Class: OTHER / Structure: OTHER / Synthetic: No|
Sequence: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI ...Sequence:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGGGPLGMSG RGKQGGKARA KAKSRSSRAG LQFPVGRVHR LLRKGNYAER VGAGAPVYMA AVLEYLTAEI LELAGNAARD NKKTRIIPRH LQLAIRNDEE LNKLLGKVTI AQGGVLPNIQ AVLLPKKTES HHKAKGKMPE PAKSAPAPKK GSKKAVTKAQ KKDGKKRKRS RKESYSVYVY KVLKQVHPDT GISSKAMGIM NSFVNDIFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SSKATCAGAA TCCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCGATAT CGATGTATAT ATCTGACACG TGCCTGGAGA CTAGGGAGTA ATCCCCTTGG CGGTTAAAAC GCGGGGGACA GCGCGTACGT GCGTTTAAGC GGTGCTAGAG CTGTCTACGA CCAATTGAGC GGCCTCGGCA CCGGGATTCT GAT
|Source||Species: Homo sapiens (human)|
|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: 84000|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF|
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