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- EMDB-18246: Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex -
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Open data
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Basic information
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Title | Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex | |||||||||
![]() | Local resolution filtered map used for model refinement | |||||||||
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![]() | Kinetochore / microtubule / error correction / chromosome segregation / CELL CYCLE | |||||||||
Function / homology | ![]() mitotic spindle polar microtubule / 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 midzone ...mitotic spindle polar microtubule / 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 midzone / attachment of spindle microtubules to kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / spindle pole body / protein localization to kinetochore / positive regulation of microtubule polymerization / mitotic spindle organization / chromosome segregation / spindle microtubule / mitotic spindle / kinetochore / spindle pole / microtubule / cell division / protein-containing complex binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
![]() | Muir KW / Barford D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Authors: Kyle W Muir / Christopher Batters / Tom Dendooven / Jing Yang / Ziguo Zhang / Alister Burt / David Barford / ![]() Abstract: Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until ...Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.2 KB 31.2 KB | Display Display | ![]() |
Images | ![]() | 60.8 KB | ||
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() | 119.9 MB 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 885.1 KB | Display | ![]() |
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Full document | ![]() | 884.7 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q84MC ![]() 8q85C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local resolution filtered map used for model refinement | ||||||||||||||||||||
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: Unsharpened 3D reconstruction
File | emd_18246_additional_1.map | ||||||||||||
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Annotation | Unsharpened 3D reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18246_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18246_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Outer kinetochore Dam1 protomer dimer with staple and Ndc80-Nuf2 ...
+Supramolecule #1: Outer kinetochore Dam1 protomer dimer with staple and Ndc80-Nuf2 ...
+Macromolecule #1: Kinetochore protein NDC80
+Macromolecule #2: Kinetochore protein NUF2
+Macromolecule #3: DASH complex subunit DAM1
+Macromolecule #4: DASH complex subunit DUO1
+Macromolecule #5: DASH complex subunit DAD2
+Macromolecule #6: DASH complex subunit DAD1
+Macromolecule #7: DASH complex subunit DAD4
+Macromolecule #8: DASH complex subunit DAD3
+Macromolecule #9: DASH complex subunit SPC34
+Macromolecule #10: DASH complex subunit ASK1
+Macromolecule #11: DASH complex subunit HSK3
+Macromolecule #12: DASH complex subunit SPC19
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 248732 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD Software: (Name: cryoSPARC (ver. 3.3.2), RELION (ver. 4.0-dev)) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2) |
-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-8q84: |