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Yorodumi- EMDB-19799: Flexible reconstruction of CBF1-CCAN bound to a centromeric CENP-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19799 | |||||||||
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Title | Flexible reconstruction of CBF1-CCAN bound to a centromeric CENP-A nucleosome (EMPIAR-11910) | |||||||||
Map data | local resolution filtered map obtained from the DynaMight half maps | |||||||||
Sample |
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Keywords | kinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
Authors | Schwab J / Kimanius D / Burt A / Dendooven T / Scheres SHW | |||||||||
Funding support | United Kingdom, 1 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. #1: Journal: biorxiv Title: DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images Authors: Schwab J / Kimanius D / Burt A / Dendooven T / Scheres SHW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19799.map.gz | 107.3 MB | EMDB map data format | |
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Header (meta data) | emd-19799-v30.xml emd-19799.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_19799.png | 84.4 KB | ||
Masks | emd_19799_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-19799.cif.gz | 4.1 KB | ||
Others | emd_19799_half_map_1.map.gz emd_19799_half_map_2.map.gz | 165.5 MB 165.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19799 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19799 | HTTPS FTP |
-Validation report
Summary document | emd_19799_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_19799_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_19799_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_19799_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19799 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19799 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19799.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local resolution filtered map obtained from the DynaMight half maps | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.853 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19799_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: unfiltered, unmasked half map reconstructed with DynaMight
File | emd_19799_half_map_1.map | ||||||||||||
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Annotation | unfiltered, unmasked half map reconstructed with DynaMight | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered, unmasked half map reconstructed with DynaMight
File | emd_19799_half_map_2.map | ||||||||||||
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Annotation | unfiltered, unmasked half map reconstructed with DynaMight | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A complex of CBF1-CCAN bound to centromeric C0N3 DNA
Entire | Name: A complex of CBF1-CCAN bound to centromeric C0N3 DNA |
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Components |
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-Supramolecule #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
Supramolecule | Name: A complex of CBF1-CCAN bound to centromeric C0N3 DNA / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100311 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |