+Open data
-Basic information
Entry | Database: PDB / ID: 8qau | |||||||||
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Title | Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex | |||||||||
Components |
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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 / attachment of spindle microtubules to kinetochore ...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 / attachment of spindle microtubules to kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / spindle pole body / protein localization to kinetochore / positive regulation of microtubule polymerization / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle / kinetochore / microtubule cytoskeleton organization / mitotic cell cycle / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Muir, K.W. / Barford, D. | |||||||||
Funding support | United Kingdom, 2items
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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, K.W. / Batters, C. / Dendooven, T. / Yang, J. / Zhang, Z. / Burt, A. / Barford, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qau.cif.gz | 266.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qau.ent.gz | 192.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qau_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8qau_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8qau_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 8qau_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/8qau ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qau | HTTPS FTP |
-Related structure data
Related structure data | 18304MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules CDE
#1: Protein | Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550 |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
#5: Protein | Mass: 38477.871 Da / Num. of mol.: 1 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 |
-Kinetochore protein ... , 2 types, 2 molecules AB
#3: Protein | Mass: 80609.375 Da / Num. of mol.: 1 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 |
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#4: Protein | Mass: 53025.949 Da / Num. of mol.: 1 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 |
-Non-polymers , 4 types, 4 molecules
#6: Chemical | ChemComp-GTP / |
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#7: Chemical | ChemComp-MG / |
#8: Chemical | ChemComp-GDP / |
#9: Chemical | ChemComp-TA1 / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Molecular weight | 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 |
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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 | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95730 / 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 | ||||||||||||||||||||||||
Refine LS restraints |
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