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Yorodumi- EMDB-17224: Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17224 | |||||||||||||||
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Title | Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | kinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE | |||||||||||||||
Function / homology | Function and homology information Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion ...Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / spindle pole body / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / chromosome, centromeric region / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / protein-containing complex binding / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Dendooven TD / Zhang Z / Yang J / McLaughlin S / Schwabb J / Scheres S / Yatskevich S / Barford D | |||||||||||||||
Funding support | United Kingdom, Germany, 4 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. Authors: Tom Dendooven / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / Johannes Schwab / Sjors H W Scheres / Stanislau Yatskevich / David Barford / Abstract: The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) ...The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A). This revealed a central CENP-A with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17224.map.gz | 77.9 MB | EMDB map data format | |
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Header (meta data) | emd-17224-v30.xml emd-17224.xml | 36.6 KB 36.6 KB | Display Display | EMDB header |
Images | emd_17224.png | 91 KB | ||
Filedesc metadata | emd-17224.cif.gz | 9.7 KB | ||
Others | emd_17224_additional_1.map.gz emd_17224_half_map_1.map.gz emd_17224_half_map_2.map.gz | 50.4 MB 65.3 MB 65.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17224 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17224 | HTTPS FTP |
-Validation report
Summary document | emd_17224_validation.pdf.gz | 1017.1 KB | Display | EMDB validaton report |
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Full document | emd_17224_full_validation.pdf.gz | 1016.7 KB | Display | |
Data in XML | emd_17224_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_17224_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17224 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17224 | HTTPS FTP |
-Related structure data
Related structure data | 8ovwMC 8ovxC 8ow0C 8ow1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17224.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.171 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_17224_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17224_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17224_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+Supramolecule #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+Macromolecule #1: Centromere-binding protein 1
+Macromolecule #3: Inner kinetochore subunit MCM16
+Macromolecule #4: Inner kinetochore subunit CTF3
+Macromolecule #5: Inner kinetochore subunit MCM22
+Macromolecule #6: Inner kinetochore subunit IML3
+Macromolecule #7: Inner kinetochore subunit CHL4
+Macromolecule #8: Inner kinetochore subunit MCM21
+Macromolecule #9: Inner kinetochore subunit CTF19
+Macromolecule #10: Inner kinetochore subunit OKP1
+Macromolecule #11: Inner kinetochore subunit CNN1
+Macromolecule #12: Inner kinetochore subunit AME1
+Macromolecule #13: Inner kinetochore subunit WIP1
+Macromolecule #14: Inner kinetochore subunit NKP1
+Macromolecule #15: Inner kinetochore subunit NKP2
+Macromolecule #2: C0N3 DNA
+Macromolecule #16: C0N3 DNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43467 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |