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Yorodumi- EMDB-0052: Masked Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0052 | |||||||||
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Title | Masked Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 | |||||||||
Map data | focused refinement of Ndc10D1-2 in CBF3 | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Zhang WJ / Lukoynova N | |||||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Authors: Wenjuan Zhang / Natalya Lukoyanova / Shomon Miah / Jonathan Lucas / Cara K Vaughan / Abstract: The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the ...The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0052.map.gz | 4.5 MB | EMDB map data format | |
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Header (meta data) | emd-0052-v30.xml emd-0052.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0052_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_0052.png | 162.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0052 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0052 | HTTPS FTP |
-Validation report
Summary document | emd_0052_validation.pdf.gz | 231.2 KB | Display | EMDB validaton report |
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Full document | emd_0052_full_validation.pdf.gz | 230.3 KB | Display | |
Data in XML | emd_0052_validation.xml.gz | 11 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0052 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0052 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0052.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | focused refinement of Ndc10D1-2 in CBF3 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Core CBF3 in complex with Ndc10 D1-2
Entire | Name: Core CBF3 in complex with Ndc10 D1-2 |
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Components |
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-Supramolecule #1: Core CBF3 in complex with Ndc10 D1-2
Supramolecule | Name: Core CBF3 in complex with Ndc10 D1-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length ...Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2. |
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Molecular weight | Theoretical: 286 KDa |
-Supramolecule #2: Cep3 homodimer
Supramolecule | Name: Cep3 homodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #3: Skp1
Supramolecule | Name: Skp1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: modified pRS424 and pRS426 |
-Supramolecule #4: Ctf13
Supramolecule | Name: Ctf13 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #5: Ndc10 comprising domains 1-2
Supramolecule | Name: Ndc10 comprising domains 1-2 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | 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
Concentration | 0.15 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I | ||||||||||||
Details | The sample is homogeneous and well-dispersed on grids. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2003 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | "Fit in map" function used to place 6FE8 and 4ACO with out further refinement or model building |
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