+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18304 | |||||||||
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Title | Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex | |||||||||
Map data | 3D flex reconstruction | |||||||||
Sample |
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Keywords | Kinetochore / microtubule / error correction / chromosome segregation / CELL CYCLE | |||||||||
Function / homology | Function and homology information mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / meiotic chromosome segregation / mitotic spindle pole body ...mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / meiotic chromosome segregation / mitotic spindle pole body / attachment of spindle microtubules to kinetochore / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / positive regulation of microtubule polymerization / mitotic spindle organization / chromosome segregation / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / kinetochore / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Muir KW / Barford D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Biorxiv / Year: 2023 Title: Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction Authors: Muir KW / Batters C / Dendooven T / Yang J / Zhang Z / Burt A / Barford D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18304.map.gz | 96.7 MB | EMDB map data format | |
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Header (meta data) | emd-18304-v30.xml emd-18304.xml | 29.6 KB 29.6 KB | Display Display | EMDB header |
Images | emd_18304.png | 52.6 KB | ||
Filedesc metadata | emd-18304.cif.gz | 7.9 KB | ||
Others | emd_18304_additional_1.map.gz emd_18304_additional_2.map.gz emd_18304_additional_3.map.gz emd_18304_additional_4.map.gz emd_18304_half_map_1.map.gz emd_18304_half_map_2.map.gz | 11.2 MB 11.2 MB 4.3 MB 51.3 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18304 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18304 | HTTPS FTP |
-Validation report
Summary document | emd_18304_validation.pdf.gz | 975.2 KB | Display | EMDB validaton report |
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Full document | emd_18304_full_validation.pdf.gz | 974.8 KB | Display | |
Data in XML | emd_18304_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_18304_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18304 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18304 | HTTPS FTP |
-Related structure data
Related structure data | 8qauMC 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_18304.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 3D flex reconstruction | ||||||||||||||||||||
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
-Additional map: 3D flex halfmap A
File | emd_18304_additional_1.map | ||||||||||||
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Annotation | 3D flex halfmap A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D flex halfmap B
File | emd_18304_additional_2.map | ||||||||||||
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Annotation | 3D flex halfmap B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local resolution filtered 3D flex map
File | emd_18304_additional_3.map | ||||||||||||
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Annotation | Local resolution filtered 3D flex map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement reconstruction
File | emd_18304_additional_4.map | ||||||||||||
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Annotation | Local refinement reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local refinement half map B
File | emd_18304_half_map_1.map | ||||||||||||
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Annotation | Local refinement half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local refinement half map A
File | emd_18304_half_map_2.map | ||||||||||||
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Annotation | Local refinement half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex ...
+Supramolecule #1: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex ...
+Macromolecule #1: Tubulin alpha-1A chain
+Macromolecule #2: Tubulin beta chain
+Macromolecule #3: Kinetochore protein NDC80
+Macromolecule #4: Kinetochore protein NUF2
+Macromolecule #5: DASH complex subunit DAM1
+Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #9: TAXOL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL In silico model: Sub-volume extracted from larger outer kinetochore microtubule consensus volume |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95730 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Initial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX |
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 540.98 |
Output model | PDB-8qau: |