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Yorodumi- EMDB-18666: Structure of the y-Tubulin Small Complex (yTuSC) as part of the n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18666 | ||||||||||||
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Title | Structure of the y-Tubulin Small Complex (yTuSC) as part of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at the spindle pole body | ||||||||||||
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Sample |
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Keywords | Microtubule nucleation / MTOC / y-tubulin / SPB / CELL CYCLE | ||||||||||||
Function / homology | Function and homology information nuclear migration by microtubule mediated pushing forces / nuclear division / mitotic spindle pole body / equatorial microtubule organizing center / nuclear migration along microtubule / homologous chromosome segregation / microtubule minus-end binding / Platelet degranulation / gamma-tubulin complex / meiotic spindle organization ...nuclear migration by microtubule mediated pushing forces / nuclear division / mitotic spindle pole body / equatorial microtubule organizing center / nuclear migration along microtubule / homologous chromosome segregation / microtubule minus-end binding / Platelet degranulation / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / spindle pole body / gamma-tubulin binding / tubulin complex / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule organization / nuclear periphery / mitotic spindle organization / meiotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle pole / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.2 Å | ||||||||||||
Authors | Dendooven T / Yatskevich S / Burt A / Bellini D / Kilmartin J / Barford D | ||||||||||||
Funding support | United Kingdom, Germany, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the native γ-tubulin ring complex capping spindle microtubules. Authors: Tom Dendooven / Stanislau Yatskevich / Alister Burt / Zhuo A Chen / Dom Bellini / Juri Rappsilber / John V Kilmartin / David Barford / Abstract: Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the ...Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the evolutionarily conserved γ-tubulin ring complex (γTuRC). However, the molecular mechanism of nucleation remains elusive. Here we used cryo-electron tomography to determine the structure of the native γTuRC capping the minus end of a MT in the context of enriched budding yeast spindles. In our structure, γTuRC presents a ring of γ-tubulin subunits to seed nucleation of exclusively 13-protofilament MTs, adopting an active closed conformation to function as a perfect geometric template for MT nucleation. Our cryo-electron tomography reconstruction revealed that a coiled-coil protein staples the first row of α/β-tubulin of the MT to alternating positions along the γ-tubulin ring of γTuRC. This positioning of α/β-tubulin onto γTuRC suggests a role for the coiled-coil protein in augmenting γTuRC-mediated MT nucleation. Based on our results, we describe a molecular model for budding yeast γTuRC activation and MT nucleation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18666.map.gz | 873.4 KB | EMDB map data format | |
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Header (meta data) | emd-18666-v30.xml emd-18666.xml | 26.7 KB 26.7 KB | Display Display | EMDB header |
Images | emd_18666.png | 55.1 KB | ||
Filedesc metadata | emd-18666.cif.gz | 8.5 KB | ||
Others | emd_18666_additional_1.map.gz emd_18666_half_map_1.map.gz emd_18666_half_map_2.map.gz | 1.5 MB 13.7 MB 13.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18666 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18666 | HTTPS FTP |
-Validation report
Summary document | emd_18666_validation.pdf.gz | 697.6 KB | Display | EMDB validaton report |
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Full document | emd_18666_full_validation.pdf.gz | 697.1 KB | Display | |
Data in XML | emd_18666_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | emd_18666_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18666 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18666 | HTTPS FTP |
-Related structure data
Related structure data | 8qv3MC 8qv0C 8qv2C 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_18666.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 3.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Map filtered with OccuPy
File | emd_18666_additional_1.map | ||||||||||||
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Annotation | Map filtered with OccuPy | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18666_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18666_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : y-Tubulin Small Complex bound to two Alpha/Beta tubulin dimers
+Supramolecule #1: y-Tubulin Small Complex bound to two Alpha/Beta tubulin dimers
+Macromolecule #1: Tubulin gamma chain
+Macromolecule #2: Spindle pole body component
+Macromolecule #3: Spindle pole body component
+Macromolecule #4: Spindle pole body component 110
+Macromolecule #5: Tubulin alpha-1 chain
+Macromolecule #6: Tubulin beta chain
+Macromolecule #7: Unknown protein
+Macromolecule #8: Unknown protein
+Macromolecule #9: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.53 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 31720 |
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Extraction | Number tomograms: 364 / Number images used: 31720 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |