[English] 日本語
Yorodumi- PDB-8q84: Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q84 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex | |||||||||
Components |
| |||||||||
Keywords | CELL CYCLE / Kinetochore / microtubule / error correction / chromosome segregation | |||||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Muir, K.W. / Barford, D. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Science / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q84.cif.gz | 608.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q84.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8q84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q84_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8q84_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8q84_validation.xml.gz | 72 KB | Display | |
Data in CIF | 8q84_validation.cif.gz | 122 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/8q84 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/8q84 | HTTPS FTP |
-Related structure data
Related structure data | 18246MC 8q85C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Saccharomyces cerevisiae (brewer's yeast) Gene: NDC80 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40460 #2: Protein | Mass: 53025.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33895 |
---|
-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.) Saccharomyces cerevisiae (brewer's yeast) Gene: DAM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53267 #4: Protein | Mass: 27515.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DUO1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53168 #5: Protein | Mass: 15084.501 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DAD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36162 #6: Protein | Mass: 10522.616 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DAD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12248 #7: Protein | Mass: 8164.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DAD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P69851 #8: Protein | Mass: 10862.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DAD3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P69850 #9: Protein | Mass: 34131.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPC34 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36131 #10: Protein | Mass: 32106.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ASK1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35734 #11: Protein | Mass: 8097.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HSK3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P69852 #12: Protein | Mass: 18935.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPC19 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03954 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Outer kinetochore Dam1 protomer dimer with staple and Ndc80-Nuf2 coiled-coils Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 673772.36 / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|