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- PDB-8q84: Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q84 | |||||||||
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Title | Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex | |||||||||
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Function / homology | ![]() mitotic spindle polar microtubule / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Muir, K.W. / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 608.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 18246MC ![]() 8q85C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Kinetochore protein ... , 2 types, 4 molecules AFBG
#1: Protein | ![]() Mass: 80609.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: NDC80 / Production host: ![]() ![]() #2: Protein | ![]() Mass: 53025.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: NUF2 / Production host: ![]() ![]() |
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-DASH complex subunit ... , 10 types, 21 molecules IUeJVKWLXMYNZOaPbQcRd
#3: Protein | Mass: 38477.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DAM1 / Production host: ![]() ![]() #4: Protein | Mass: 27515.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DUO1 / Production host: ![]() ![]() #5: Protein | Mass: 15084.501 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DAD2 / Production host: ![]() ![]() #6: Protein | Mass: 10522.616 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DAD1 / Production host: ![]() ![]() #7: Protein | Mass: 8164.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DAD4 / Production host: ![]() ![]() #8: Protein | Mass: 10862.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DAD3 / Production host: ![]() ![]() #9: Protein | Mass: 34131.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: SPC34 / Production host: ![]() ![]() #10: Protein | Mass: 32106.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ASK1 / Production host: ![]() ![]() #11: Protein | Mass: 8097.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HSK3 / Production host: ![]() ![]() #12: Protein | Mass: 18935.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: SPC19 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Outer kinetochore Dam1 protomer dimer with staple and Ndc80-Nuf2 coiled-coils Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 673772.36 / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 248732 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 540.98 / Protocol: OTHER / Space: REAL Details: Initial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX | ||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 540.98 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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