+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4579 | ||||||||||||
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Title | Structure of inner kinetochore CCAN-Cenp-A complex | ||||||||||||
Map data | Map of CCAN-Cenp-A | ||||||||||||
Sample |
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Keywords | inner kinetochore / DNA / nucleosome / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation ...2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / spindle attachment to meiosis I kinetochore / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / attachment of spindle microtubules to kinetochore / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / CENP-A containing chromatin assembly / HDACs deacetylate histones / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / spindle pole body / protein localization to kinetochore / replication fork protection complex / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / postreplication repair / SUMOylation of chromatin organization proteins / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / rRNA transcription / Estrogen-dependent gene expression / DNA replication initiation / localization / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / heterochromatin organization / nucleosomal DNA binding / mitotic spindle organization / meiotic cell cycle / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / sequence-specific DNA binding / protein heterodimerization activity / cell division / DNA repair / protein-containing complex binding / regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast) / Escherichia coli (E. coli) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
Authors | Yan K / Yang J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nature / Year: 2019 Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford / Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation. | ||||||||||||
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_4579.map.gz | 10.1 MB | EMDB map data format | |
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Header (meta data) | emd-4579-v30.xml emd-4579.xml | 38.9 KB 38.9 KB | Display Display | EMDB header |
Images | emd_4579.png | 38.6 KB | ||
Filedesc metadata | emd-4579.cif.gz | 8.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4579 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4579 | HTTPS FTP |
-Validation report
Summary document | emd_4579_validation.pdf.gz | 219.9 KB | Display | EMDB validaton report |
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Full document | emd_4579_full_validation.pdf.gz | 219 KB | Display | |
Data in XML | emd_4579_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4579 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4579 | HTTPS FTP |
-Related structure data
Related structure data | 6qldMC 4580C 4581C 4971C 6qleC 6qlfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4579.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of CCAN-Cenp-A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
+Supramolecule #1: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
+Supramolecule #2: kinetochore
+Supramolecule #3: DNA
+Supramolecule #4: Histones
+Macromolecule #1: Inner kinetochore subunit MIF2
+Macromolecule #3: Inner kinetochore subunit MCM16
+Macromolecule #4: Inner kinetochore subunit CTF3
+Macromolecule #6: Inner kinetochore subunit MCM22
+Macromolecule #7: Inner kinetochore subunit IML3
+Macromolecule #8: Inner kinetochore subunit CHL4
+Macromolecule #9: Inner kinetochore subunit MCM21
+Macromolecule #10: Inner kinetochore subunit CTF19
+Macromolecule #11: Inner kinetochore subunit OKP1
+Macromolecule #12: Inner kinetochore subunit AME1
+Macromolecule #13: Inner kinetochore subunit NKP1
+Macromolecule #14: Inner kinetochore subunit NKP2
+Macromolecule #15: Histone H3-like centromeric protein CSE4
+Macromolecule #16: Histone H4
+Macromolecule #17: Histone H2B.2
+Macromolecule #18: Histone H3-like centromeric protein CSE4
+Macromolecule #19: Histone H2A.1
+Macromolecule #20: Histone H2B.1
+Macromolecule #21: Histone H2A.1
+Macromolecule #2: DNA (125-MER)
+Macromolecule #5: DNA (125-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 32.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Reconstruction using SIMPLE_prime |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145783 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |