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Yorodumi- EMDB-30237: The cryo-EM structure of CENP-A nucleosome in complex with CENP-C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30237 | ||||||||||||
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Title | The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain | ||||||||||||
Map data | ggCENP-A nucleosome in complex with CENP-C peptide (643-683) and CENP-N (1-212) | ||||||||||||
Sample |
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Keywords | CENP-A nucleosome / CENP-C / CENP-N / complex / kinetochore / NUCLEAR PROTEIN / CELL CYCLE-DNA complex | ||||||||||||
Function / homology | Function and homology information kinetochore => GO:0000776 / Interleukin-7 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Chromatin modifying enzymes / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence ...kinetochore => GO:0000776 / Interleukin-7 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Chromatin modifying enzymes / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / B-WICH complex positively regulates rRNA expression / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / spindle attachment to meiosis I kinetochore / CENP-A containing chromatin assembly / centromeric DNA binding / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / detection of maltose stimulus / maltose transport complex / maltose binding / establishment of mitotic spindle orientation / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / mitotic cytokinesis / chromosome, centromeric region / carbohydrate transmembrane transporter activity / negative regulation of megakaryocyte differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / ATP-binding cassette (ABC) transporter complex / DNA methylation / cell chemotaxis / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / chromosome segregation / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Meiotic recombination / kinetochore / Metalloprotease DUBs / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide Similarity search - Function | ||||||||||||
Biological species | Ectocarpus siliculosus (eukaryote) / Homo sapiens (human) / Escherichia coli (strain B / BL21-DE3) (bacteria) / Gallus gallus (chicken) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Ariyoshi M / Makino F | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C. Authors: Mariko Ariyoshi / Fumiaki Makino / Reito Watanabe / Reiko Nakagawa / Takayuki Kato / Keiichi Namba / Yasuhiro Arimura / Risa Fujita / Hitoshi Kurumizaka / Ei-Ichi Okumura / Masatoshi Hara / Tatsuo Fukagawa / Abstract: The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a ...The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a kinetochore. CENP-C and CENP-N are CENP-A binding proteins. We previously demonstrated that vertebrate CENP-C binding to the CENP-A nucleosome is regulated by CDK1-mediated CENP-C phosphorylation. However, it is still unknown how the phosphorylation of CENP-C regulates its binding to CENP-A. It is also not completely understood how and whether CENP-C and CENP-N act together on the CENP-A nucleosome. Here, using cryo-electron microscopy (cryo-EM) in combination with biochemical approaches, we reveal a stable CENP-A nucleosome-binding mode of CENP-C through unique regions. The chicken CENP-C structure bound to the CENP-A nucleosome is stabilized by an intramolecular link through the phosphorylated CENP-C residue. The stable CENP-A-CENP-C complex excludes CENP-N from the CENP-A nucleosome. These findings provide mechanistic insights into the dynamic kinetochore assembly regulated by CDK1-mediated CENP-C phosphorylation. | ||||||||||||
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_30237.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-30237-v30.xml emd-30237.xml | 32.7 KB 32.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30237_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_30237.png | 120.3 KB | ||
Masks | emd_30237_msk_1.map | 27 MB | Mask map | |
Filedesc metadata | emd-30237.cif.gz | 8 KB | ||
Others | emd_30237_half_map_1.map.gz emd_30237_half_map_2.map.gz | 19.8 MB 19.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30237 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30237 | HTTPS FTP |
-Validation report
Summary document | emd_30237_validation.pdf.gz | 878.9 KB | Display | EMDB validaton report |
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Full document | emd_30237_full_validation.pdf.gz | 878.4 KB | Display | |
Data in XML | emd_30237_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_30237_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30237 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30237 | HTTPS FTP |
-Related structure data
Related structure data | 7bxtMC 7by0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10571 (Title: The cryo-EM structure of the CENP-A nucleosome in complex with the phosphorylated CENP-C:: CENP-A nucleosome in complex with CENP-C motif (655-675) and CENP-N N-terminal domain (1-211) Data size: 1.3 TB Data #1: CENP-A nucleosome in complex with CENP-C motif (655-675) and CENP-N N-terminal domain (1-211) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30237.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ggCENP-A nucleosome in complex with CENP-C peptide (643-683) and CENP-N (1-212) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_30237_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: 1st half map file for ggCENP-A nucleosome in...
File | emd_30237_half_map_1.map | ||||||||||||
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Annotation | 1st half map file for ggCENP-A nucleosome in complex with CENP-C peptide (643-683) and CENP-N (1-212) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 1st half map file for ggCENP-A nucleosome in...
File | emd_30237_half_map_2.map | ||||||||||||
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Annotation | 1st half map file for ggCENP-A nucleosome in complex with CENP-C peptide (643-683) and CENP-N (1-212) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CENP-A nucleosome in complex with CENP-C peptide and CNEP-N N-ter...
+Supramolecule #1: CENP-A nucleosome in complex with CENP-C peptide and CNEP-N N-ter...
+Supramolecule #2: Histone H3,Histone H3-like centromeric protein A
+Supramolecule #3: Histone H4
+Supramolecule #4: Histone H2A type 1-B/E
+Supramolecule #5: Histone H2B type 2-E
+Supramolecule #6: DNA
+Supramolecule #7: CENP-C
+Supramolecule #8: Maltodextrin-binding protein,Centromere protein N
+Macromolecule #1: Histone H3,Histone H3-like centromeric protein A
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 2-E
+Macromolecule #7: CENP-C
+Macromolecule #8: Maltodextrin-binding protein,Centromere protein N
+Macromolecule #5: DNA (145-mer)
+Macromolecule #6: DNA (145-mer)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Details: Both side | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 5 / Number real images: 5346 / Average exposure time: 10.0 sec. / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Calibrated defocus max: -7.0 µm / Calibrated defocus min: -0.5 µm / Calibrated magnification: 45454 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |